1. Water and bonding Flashcards
what type of elements make up 97% of the weight in most organisms? What is another name for them?
nonmetallic elements
called bulk elements
how many bulk elements are there? What are they?
there are 6:
C, H, N, O, P, S
what are the elements called that make up the remaining 3% of weight in living organisms?
they’re called trace elements
list the 5 essential trace elements
Ca2+, K+, Na+, Mg2+, Cl-
what are three possible shapes of covalently linked carbon chains
linear, branched, cyclic
how are macromolecules assembled
assembled from smaller and simper monomeric precursors
how are monomeric units usually held together
via covalent bonds
T or F: Supramolecular complexes are held together by covalent bonds
False! They’re held together via non-covalent interactions
List the non-covalent interactions that hold together supramolecular complexes
hydrogen bonds, ionic interactions, hydrophobic effect, and van der Waals forces
what is the role of a functional group
functional groups help confer the chemical properties of a molecule
describe “conformation”
conformations are due to bond rotation of a molecule. No bonds are broken, but different spatial arrangement creates stereoisomers
define stereoisomers
molecules with the same chemical formula and bonds, but different fixed arrangements of atoms
describe “configuration”
a configuration is a different arrangement of the atoms in a molecule, due to the breakage of bonds
T or F: a double bond cannot rotate
true
since double bonds cannot rotate, can geometric (cis/trans) isomers have different conformations?
No, only configurations, because we cannot rotate so bonds would have to be broken
what is a chiral carbon
a carbon bound to 4 different groups
for each chiral carbon, how many stereoisomers can there be
2
define enantiomers
two molecules that are mirror images of each other (non superimposable)
define diastereomers
molecules are diastereomers if they are not enantiomers
how much mass does water account for in most cells
60-90%
what about water molecules influence the cell structure and properties of all cell components?
the attractive forces between water molecules and the tendency of water to ionize
T or F: water’s strength as a solvent influences the strength and specifics of interactions between biomolecules
true
how does water as a solvent differ from other solvents?
water has the highest mp, bp, heat of vaporization, and specific heat
define specific heat
specific heat is the energy input required to raise the temperature by 1 degree
what are the four types of weak interactions that are important for the function and structure of water
hydrogen bonds, charge-charge interactions, Van der Waals forces, and hydrophobic effect
what are 3 important functions of water for life on earth
cohesion, density, solvent
how many electrons does a water molecule have
8
where are the 8 electrons of a water molecule located within the molecule
the oxygen has 6, and these are in the outer shell, each H has 1
what orbitals do the 6 oxygen electrons occupy
four sp3 hybrid orbitals
what is the shape of a water molecule? why?
a tetrahedron; formed by the four sp3 hybrid orbitals
describe the corners of a tetrahedron water molecule
two corners have H’s, two corners have lone paired electrons
what are the bond angles of a perfect tetrahedron?
109.5 degrees
what are the bond angles of a water molecule tetrahedron
104.5 degrees
why are the bond angles of water smaller than that of a perfect tetrahedron?
the oxygen nucleus attracts electrons more strongly than the hydrogen nucleus. The shared electrons in the O-H bonds spend more time near O than near H, so this unequal sharing results in two electric dipoles
what charge does each atom in a water molecule have due to the dipoles
oxygen has a partial negative charge (g-) and hydrogens have a partial positive charge (g+)
what makes a molecule polar
the presence of a net dipole
in what directions on the periodic table does electronegativity increase
increases to the right and up
T or F: hydrogen bonds are weaker than covalent bonds
true! they’re ~20 times weaker
T or F: hydrogen bonds are shorter than covalent bonds
false! they’re ~2 times longer
describe the lifetime of a hydrogen bond
lasts 10-12 seconds, constantly associating and disassociating (ie flickering)
T or F: the sum of all the hydrogen bonds confers great internal strength to liquid water
true
how many hydrogen bonds can water form in ice
4
why is there a high melting point of water
because water in ice can form 4 hydrogen bonds, and it requires much thermal energy to break so many
T or F: it is very easy to break the 4 hydrogen bonds of ice to melt it
false! it requires much thermal energy to break these bonds and melt ice
how many hydrogen bonds are formed in liquid water
3.4, because water is less organized and in continuous motion
why does liquid water form only 3.4 hydrogen bonds as compared to ice which forms 4?
liquid water is less organized and in continuous motion, so it only forms 3.4 hydrogen bonds
what structure does ice have
a lattice structure
T or F: water atoms are more spread out in a lattice structure
true
since water atoms are more spread out in a lattice structure (ice), what does this mean about the density
ice is less dense than water
describe a hydrogen bond
it’s a bond between an electronegative atom and hydrogen (but the hydrogen must be COVALENTLY bound to it’s own electronegative atom)
in a hydrogen bond, what does it mean that the H needs to be covalently bound to it’s own electronegative atom before it can create the hydrogen bond?
the H must be covalently bound to its own electronegative atom, meaning it must have a partial positive charge (must be POLAR)
in what shape are hydrogen bonds the strongest
strongest when they’re linear
why are hydrogen bonds strongest when they’re linear
this maximizes the electrostatic attraction between the atoms
T or F: there is a stronger interaction between water molecule’s at the water-air interface
true
explain why there’s a stronger interaction between water molecules at the water-air interface
water molecules that aren’t at the surface form hydrogen bonds in all directions. Water molecules at the surface only have hydrogen bonds in 3 directions, so they become more strongly bound to the water molecules beside them
what is the result of water molecules having a stronger interaction at the water-air interface?
surface tension
what are charge-charge interactions
these are electrostatic interactions between two charged particles (including ionic bonds)
T or F: charge-charge interactions are the weakest noncovalent forces
false! they’re potentially the strongest noncovalent forces
T or F: charge-charge interactions extend over greater distances than other noncovalent forces
true
how are salt bridges formed in many proteins
formed when there are charge-charge interactions between oppositely charges protein side chains (R groups)
T or F: most biomolecules are either polar or charged
true
what are examples of biomolecules that are polar/charged
sugars and amino acids
what solvent easily dissolves most biomolecules
water
how does water dissolve salts?
does so by hydrating the ions, which weakens the electrostatic interactions between them
T or F: salts have a greater entropy when dissolved
true; when dissolved, they have much greater freedom of movement = greater entropy
T or F: water is effective at screening electrostatic interactions as a solvent
true
what is the outcome of water being effective of screening electrostatic interactions as a solvent
it is good at dissolving salts and hydrophilic biomolecules
why is water effective at screening electrostatic interactions as a solvent?
it has a high dielectric constant (ε)
what is the formula for strength of ionic interactions in a solution? what does each part mean
F=(Q1Q2)/er2 F=strength of ionic interactions in a solution Q=magnitude of charges e=dielectric constant of the solvent r=distance between charged groups
T or F: as the dielectric constant of the solvent gets larger (ie in water it’s large), F gets smaller
true; the higher the dielectric constant, the weaker the ionic interactions in a solution
what are the 3 key gases in this course
N2, O2, and CO2
do N2, O2, or CO2 have net dipoles
no net dipole
are N2, O2, and CO2 soluble in water?
no, they’re poorly soluble in water
how does maximizing the entropy of water help drive substrate-enzyme interactions
when water=ordered, molecules surround both substrate and enzyme, blocking them from joining. When water is unordered, it becomes displaced so the enzyme and substrate can interact
what types of bonds help stabilize an enzyme-substrate complex
hydrogen bonds, ionic bonds, and hydrophobic interactions
describe the hydrophobic effect
non-polar segments constrain adjacent water molecules into a highly ordered cage, reducing entropy
is entropy high or low due to the hydrophobic effect
low entropy (water is assembled into a highly ordered cage)
what happens to enthalpy due to the hydrophobic effect? how is this caused
enthalpy increases; the non-polar segments disrupt hydrogen bonds between water molecules
what happens when an amphipathic molecule is in water
it tends to assemble in the manner which will shield the non-polar regions as much as possible from water, keeping entropy as high as possible
describe 3 ways amphipathic molecules can assemble in water
dispersion of lipids, clusters of lipids, or micelles
describe Van der Waals interactions
when two uncharged atoms are brought close together, the surrounding electron clouds influence each other and can form transient electric dipoles in adjacent molecules
how does distance affect Van der Waals forces
if the two nuclei are too far apart, electron clouds won’t influence each other, and if they’re too close the electron clouds will repel each other
T or F: Van der Waals forces are very strong
false; they’re weak
use radii to explain why covalent bonds are stronger than Van der Waals forces
when two atoms are covalently joined, the atomic radii are shorter than the Van der Waals radii
short radii=stronger attraction
why are water molecules essential for a substrate to bind properly to an active site of an enzyme
water molecules help connect components of the active site (ie sugar) to certain amino acid residues on the substrate
why is water important to cells in regards to temperature
water has a high specific heat, so it takes a lot of energy to raise or lower the temperature. Since cells contain a huge amount of water, the temperature of cells stays more consistent
