Download Problem Set 1 Key

Problem Set 1-Answer Key
BILD1 SP16
1) Using water as an example, explain what a polar molecule is. Using the
stick diagram, label which atoms are positively or negatively polarized.
Water, is a compound, that has a very electronegative (pulls electrons
towards itself) atom ,Oxygen, that is covalently bonded to 2 Hydrogen
atoms (not very electronegative), As a consequence of these covalent bonds
– the shared electrons are pulled toward the Oxygen atom and causes
Hydrogen to become positively (+) polarized. Oxygen, having drawn the the
shared pair of electrons towards itself, becomes negatively polarized. The
symbol - δ+ and δ- is used to depict positively and negatively polarized atoms,
respectively.
δ-
O
δ+
H
δ+H
NOTE: Because water is polar – it can H-Bond.
2) For each molecule shown, decide if it can accept a hydrogen bond, donate
a hydrogen bond, do both, or do neither. Circle the H that acts as a donor H.
Indicate the H’s that can not participate in H bonding with an arrow.
a) Donate and Accept
(Oxygen accepts)
a) CH3- CH20H
c) Donate and Accept
(Nitrogen and oxygen
accepts)
c) CH3- NH-CO-CH3
e) Donate and Accept
(Oxygen accepts)
e) CH3- CH0H-CHOH- CH3
b) Accept only
(Oxygen accepts)
b) CH3-0- CH3
d) No donor, no acceptor
d) CH3- CH2- CH2- CH3
f) No donor, no acceptor
f) H2
= Hydrogen that can not participate in H-Bonds
= Donor Hydrogen
3) Look at the molecules listed below. a) Which of the molecules are
hydrophobic? b) Which are hydrophilic? c) Which are amphipathic? d)
Which molecules can ionize? e) Write each of the molecules in molecular
short hand (I will give you one (D)).
A)
B)
C)
D)
E)
E is hydrophobic
A, B, and C are hydrophilic
D is amphipathic
B, C, and D can ionize
(Note- this exercise is to help familiarize yourself with how organic
molecules are written in shorthand – key is to identify functional
grounds that makes molecules, hydrophobic, hydrophiic, polar,
nonpolar, can ionized, etc.)
4) HCl is a strong acid. What distinguishes a strong acid from a weak one?
Describe the pH scale. What would be the pH of a 0.1 M solution of HCl?
What would be the concentration of OH- in this solution?
Strong acids completely dissociate to their ionic form in water (e.g. H+ and
Cl- ions). Weak acids partially dissociate, and the binding and release of H+
ions is reversible (Carbonic acids was used as a example in class). pH scale
compresses the range of [H=] and [OH-] by employing logarithms – pH
declines as the [H+] increases ([OH-] decreases) and pH increases as [H+]
decreases ([OH-] increases) The pH of 0.1 M solution of HCL is 1
[H+] = - log 10-1 M = -(-1) = 1; [OH-] is 10-13 M (10-1 x 10-13 equal 10-14)
5) Each of the molecules below is placed into an aqueous buffered solution
(pH ~ 7.0). What would be the net negative charge of each molecule in
solution? Indicate the charged functional group with the charge it will have
at those conditions (This is not as hard as you think – think about the
functional groups!).
-1
a) CH3- CH2-CH2-CH2-CH2-COOH
minus 1 net
b) CH3- CH2-CH2-CH2-CH2-CHO
no net charge
-1
+1
c) NH2-CH2-CH2-CH2-COOH
no net charge
-1
d) CH3-O-HPO2-O- CH2- CH3
-2
+1
minus 1 net
e) H2PO4- CH2- CH2- NH2
minus 1 net
6) Why is the fatty acid shown below considered an unsaturated fatty acid?
Indicate the fatty acid portion of the molecule, and circle the features or
features of the molecule that the term “unsaturation” refers to.
This fatty acid is unsaturated because of the presence of double bonds
which can actually form kinks and can affect the packing of these fatty
acids (e.g. butter – saturated – solid at room temp; vegetable oil has
unsaturated fatty acids – and is liquid at room temp)
7) Write the hydrolysis reaction that would break the amide bond in
question 6 (make sure to draw the products of the reaction).
8) The pictures below are of two structures that we have discussed in class
and in the readings. a) For each, label what it is, the position of the polar
head group, and the hydrophobic groups. b) What are some of the
similarities about each type of structure? What are some of the
differences?
Similarities: both formed from amphipathic molecules, both formed by
hydrophobic interactions, both have a non-aqueous compartment or region..
Difference: micelle does not have an enclosed aqueous compartment,
bilayers do- KEY!!
10) What do all amino acids have in common? How do they differ? (Think
about the basic structure!)
Basic answer I am looking for:
They all have an amine, carboxyl, and R group.
They differ in R-group properties
Hydrophobic
Hydrophilic
Positively charged
Negatively charged
Glycine, is unique because it does not have an R-group – it has two hydrogens
covalently attached – can allow for kinks in proteins.
Proline is unique hydrocarbon (hydrophobic amino acid) because it is very
rigid
Cysteine – can form disulfide bonds
11) Look at the amino acid table in the book (Figure5.16, on page 79).
(a) Draw the dipeptide ARG-GLU.
(b) Circle the peptide bond.
(c) Which is the N-terminus? Which is the C-terminus? Demarcate them
with arrows.
(d) What is the NET charge of this dipeptide in the cell?
(e) What would the NET charge be if the amino acid PROLINE was added
to the C-terminus to form ARG-GLU-PRO?
12) If 600 amino acids are condensed to form a protein, how many peptide
bonds are being formed? How many molecules of H2O are split out during
the condensation? If the average molecular weight of a free amino acid is
130 daltons, what is the molecular weight of the protein?
599 peptide bonds formed; 599 molecules of H20 are split out; 78,000
daltons minus the loss of 599 H20 =67218 Da or 67.2 kDa.