Chem 212
Survey of Organic and Biochemistry
Spring 2006
_____________________________
Print your full name legibly in the space above.
Exam 3: Ch. 11-13
4 May 2006
Instructions:
No books or notes of any kind are permitted. You may borrow a model kit. Put all your answers on this exam paper. If you
want something graded which is written on scratch paper, you must indicate so in the regular space for the answer.
Good Luck!
1.
(7 pts) Below each of the following structures, write all of the appropriate terms from the list: triose, tetrose, pentose,
hexose, heptose, aldose, ketose, aldonic acid, uronic acid, alditol, pyranose, furanose, “”, “”, amino, N-acetyl, deoxy,
phosphate ester. (Give the carbon number for amino, N-acetyl, deoxy, and phosphate!)
O
H
HO
OH
HO
H
HO
H
H
OH
O
O OH
OH
OH
HO
OH
O
OH
HO
OH
HO
OH
OH
O
O
OH HO
OH
HO
H
NH
OH
H
H
OH
OH
OPO 3H 2
OH
O
OH
#carbons:
hexose
hexose
hexose
heptose
tetrose
triose
funct. grp.:
uronic acid
ketose
aldose
ketose
aldonic acid
alditol
ring size:
pyranose
furanose
pyranose
ring stereo:
(none)


derivative

5-deoxy

4-N-acetyl-amino
3-phosphate
Notes: “uronic acid” implies presence of aldehyde at carbon 1, so there is no need (but it is not incorrect) to also call it an aldose. For the
last structure, the 3-phosphate could be called a 1-phosphate since there is no way to know which carbon is number 1 except by the way it
happens to be drawn above. The  for the third structure is correct because OH is cis to the CH2OH;  and  refer to the cis/trans
relationship, not to the up or down direction of the OH in the Haworth projection.
2. (6 pts) Draw Fisher projections for of all the 2-ketopentoses (open chain form) and indicate which are D and which are L.
OH
OH
OH
O
O
O
OH
HO
O
HO
OH
OH
OH
OH
OH
D
OH
HO
HO
OH
OH
D
L
L
Direction of the first and last OH and of the C=O at carbon 2 is irrelevant because those positions are not stereocenters
3.
(3 pts) Draw the Haworth projection (i.e. the flat-ring format) for -L-Tagatofuranose
OH
HO
OH
O
OH
OH
HO
O
OH
OH
HO
HO
-D-Tagatofuranose (mirror) -L-Tagatofuranose
The easiest way to draw the L sugar is to first draw the D sugar and then reflect the structure through a mirror plane.
4.
(5 pts) What type of functional group forms when a 5-aminohexose aldonic acid cyclizes to form a 6-atom ring? Draw a
Haworth projection structure of a sugar in that form.
HO
O
OH
H
N
OH
OH
OH
O
HO
OH
When a 5-aminohexose aldonic acid cyclizes, the amino group must be the
group that attaches to the carboxylic acid to form the ring. Carboxylic acids
can combine with amines to form amides; the cyclic form of an amide is
called a lactam. Due to the size of the ring, this would be called a delta ()
lactam.
OH
NH2
OH
Page 1
Chem 212
5.
Survey of Organic and Biochemistry
Spring 2006
(8 pts) The following structure represents stachyose, an oligosaccharide is found in beans.
a. Circle and identify the individual saccharide groups in stachyose.
b. Point an arrow to each glycosidic bond and identify its type (i.e. “1,2” etc.)
c. Is this a reducing sugar? Explain your answer.
OH
-D-Galactopyranose
1,6
O
HO
This is not a reducing sugar because
there is no hemiacetal group (instead
there is an 1,2 linkage).
OH
O
OH
O
HO
-D-Galactopyranose
1,6
OH
OH
O
O
HO
-D-Gulopyranose
OH
HO
-D-Fructofuranose
OH
1,2
O
O
HO
OH
OH
6.
(6 pts) Identify the following structures as simple triglycerides, glycerophospholipids, sphingolipids, glycolipids, or
prostaglandins.
O
HN
OH
O
HO
O
OH
OH
OH
prostaglandin
7.
sphingolipid
glycolipid
(5 pts) Cholesterol has a fused four-ring steroid nucleus and is part of the body membranes. The –OH group on carbon 3
is the polar head, and the rest of the molecule provides the hydrophobic tail that does not fit into the zig-zag packing of
the hydrocarbon portion of the saturated fatty acids. Considering this structure, tell whether small amounts of cholesterol
well dispersed in the membrane contribute to the stiffening (rigidity) or fluidity of the membrane. Explain your answer.
Small amounts of cholesterol would disrupt the ordered packing of long chain saturated fatty acids in the cell
membrane because of the zig-zag structure. Consequently, the Van Der Walls or hydrophobic attractive forces between
these molecules of the membrane would be weakened, and the melting point would decrease; this also means that at a
given temperature the membrane would be more fluid.
Page 2
Chem 212
Survey of Organic and Biochemistry
Spring 2006
8.
(4 pts) Dr. Hans Selye, (1907-1982) is listed in the Canadian Medical Hall of Fame for his discovery of the role of stress
in health and disease, particularly the structures of the steroids involved in the stress response. Above the keystone of his
house in Montreal, he carved the four-ring parent structure for all steroids. Draw that structure below.
9.
(5 pts) Briefly describe how aspirin and other NSAIDs reduce inflammation, but also may cause stomach ulcers.
NSAIDS (Non Steroidal Anti Inflammatory Drugs) block the enzyme cyclooxygenase (COX), which converts
arachidonic acid into prostaglandins. Prostaglandins are ubiquitous hormones, and among other things they control
inflammation. However, prostaglandins in the stomach also protect the stomach lining, and inhibition of that hormone
in the stomach can lead to ulcers.
10. (6 pts) What are the two roles of bile salts in the body?
Bile salts are the breakdown products of steroids, so they are the way the body eliminates steroids. They also act as
detergents, in other words, they help dissolve the fats in the intestine so they can be absorbed.
11. (5 pts) Lipopolysaccharides are molecules found on the membrane surface of Gram-negative bacteria. The lipid
molecules anchor the polysaccharide into the membrane. They are composed of a polysaccharide with one saccharide
linked to four long chain fatty acids via ester bonds. How are lipopolysaccharides and glycolipids similar? How are they
different?
Both lipopolysaccharides and glycolipids have long chain fatty acids and are attached to carbohydrates. However, the
backbone molecule for glycolipids is sphingosine, while the backbone for the lipopolysaccharides is a saccharide
molecule. Also, glycolipids have one fatty acid linked as an amide bond to the sphingosine – which itself has a long
alkyl chain, whereas lipopolysaccharides have four fatty acids.
12. (10 pts) Draw the structure of the polypeptide represented by the sequence AGKDE at its isoelectric point.
O
O
O
H3N
+
NH
NH
O
-
O
NH
NH
O
-
O
O
+
NH3
HO
Page 3
O
The sequence has one basic (K) and two acidic (D
and E) amino acids. Along with the amino and
carboxy ends of the peptide, there would be two + and
three - charges in the structure at neutral pH. In order
to be at the isoelectric point, one of the three
carboxylates is be protonated to give a neutral
structure. It does not matter which one is protonated.
Chem 212
Survey of Organic and Biochemistry
Spring 2006
13. (10 pts) The “Bohr Effect” describes the change in ability of hemoglobin to absorb oxygen as the pH of the solution
changes. This is caused by a change in the quaternary interactions of the protein. Of the interactions you know that are
involved in quaternary structure, which type might be influenced the most by the pH of the solution? Give an example of
a pair of amino acids that interact this way, and draw their structures at low pH, physiological pH, and high pH (where
the low and high are different enough from physiological pH to see a difference). Is the interaction stronger or weaker
outside of physiological pH? Explain your answer.
H
N
His (H)
O
Glu (E)
Acidic (low pH)
N
H
+
H
N
His (H)
N
H
O
Glu (E)
+
H
N
His (H)
OH
O
O
Glu (E)
N
O
Neutral (physiological)
-
Salt bridges are most affected by pH, because the pH
can affect the charge of the side chains. Any of the
basic amino acids (K, R, H) can form a salt bridge with
either of the acidic amino acids (D, E). Under
sufficiently acidic conditions, the acid group will be
protonated, i.e. neutral, and under sufficiently basic
conditions the basic group will be deprotonated (i.e.
neutral). In either of those extremes there are not two
oppositely charged groups attracting one another.
Basic (high pH)
-
14. (8 pts) For each of these single amino-acid mutations (changes) in protein structure, describe whether or not the change is
expected to cause a significant change in the protein structure and explain your reasoning.
a. Valine changed to Leucine
Both amino acids are nonpolar and relatively bulky, so this is unlikely to cause a dramatic change in protein structure
b. Glycine changed to Isoleucine
Although both amino acids are nonpolar, glycine is the smallest amino acid side chain. If there is no room to accommodate a
larger group in the protein at this position, changing glycine to anything could disrupt the structure.
c. Methionine changed to Proline
While both of these are nonpolar, proline can not form alpha helices or beta sheets because when it is part of the peptide chain, it
does not have an NH that can hydrogen bond. Proline is also commonly found at the ends of helices or sheets as part of a turn.
Thus this change is likely to cause a significant change in protein structure.
d. Cystine changed to Methionine
Cystine is the only amino acid that can participate in covalent disulfide bonds. While methionine has a sulfur atom, it can not
make disulfide bonds. Thus this change is likely to cause a significant change in protein structurel.
15. (6 pts) Surface membrane proteins are found associated with the surface of a lipid bilayer, which generally has phosphate
groups present. What types of amino acids might be found on the exterior surface of a surface membrane protein where it
binds to the surface of the lipid bilayer? Explain your answer.
Phosphate groups are negatively charged, so the amino acids most likely to interact with these are the positively charged (basic) amino
acids histidine (H), arginine (R) and Lysine (K). In addition, any of the amino acids that can donate a hydrogen bond can also interact
with the phosphate anions. These are N, C, Q, S, T, W, and Y. The acidic amino acids D and E are negatively charged at physiological
pH and should repel from the negatively charged phosphate. Thus they are the least likely to be present at the interface between a
protein and a phosphate.
16. (6 pts) Draw structures that show a pair of amino acids interacting by:
a. Hydrophobic (van-der-walls) interaction
Phe
b.
Phe
Any two hydrophobic amino acids can interact this
way. They do not have to be the same. There is not
much to draw for a hydrophobic interaction - just
two nonpolar amino acids next to each other.
Hydrogen bonding
H
Ser
O
Ser
O
H
There are many choices of pairs of amino acids. They do
not have to be the same amino acids so long as one is a
hydrogen bond donor and one is a hydrogen bond acceptor.
Page 4
Chem 212
Survey of Organic and Biochemistry
Spring 2006
The following tables may be useful for some of the questions below:
O
O
H
H
H
H
OH
OH
OH
OH
OH
HO
H
H
H
O
H
OH
OH
OH
H
HO
H
H
O
OH
H
OH
OH
OH
HO
HO
H
H
O
H
H
OH
OH
OH
H
H
HO
H
O
OH
OH
H
OH
OH
HO
H
HO
H
OH
O
H
OH
H
OH
H
HO
HO
H
OH
H
H
OH
OH
D-Allose D-Altrose D-Glucose D-Mannose D-Gulose
D-Idose
OH
HO
HO
HO
H
O
OH
OH
OH
H
H
H
OH
O
OH
OH
OH
O
H
OH
OH
O
OH
H
OH
H
H
H
OH
HO
H
H
OH
D-Galactose D-Talose
H
HO
H
OH
OH
+
NH
+
SH
NH2
CH3
COO
H 3N
O
O
+
Alanine (Ala, A)
O
Arginine (Arg, R)
O
OH
OH
NH2
COO
H 3N
+
H 3N
COO
Asparagine (Asn, N)
+
H 3N
COO
Aspartic acid (Asp, D)
NH2
+
COO
Glutamic acid (Glu, E)
+
H 3N
COO
Glutamine (Gln, Q)
+
COO
H 3N
Glycine (Gly, G)
COO
Cystine (Cys, C)
+
H 3N
COO
CH3
H3C
+
COO
H 3N
Histidine (His, H)
Isoleucine (Ile, I)
H3C
+
CH3
+
H 3N
N
N
H
H 3N
S
H 3N
CH3
+
H 3N
COO
Leucine (Leu, L)
+
H 3N
COO
Lysine (Lys, K)
+
H 3N
COO
Methionine (Met, M)
+
H 3N
COO
+
NH 2
Phenylalanine (Phe, F)
COO
Proline (Pro, P)
OH
OH
H3C
H3C
OH
CH3
N
H
+
H 3N
COO
Serine (Ser, S)
+
H 3N
COO
Threonine (Thr, T)
+
H 3N
COO
Tryptophan (Trp, W)
Page 5
+
H 3N
HO
HO
H
O
H
H
OH
OH
D-Psicose D-Fructose D-Sorbose D-Tagatose
The 20 Common Amino Acids
(in alphabetical order)
H 2N
OH
COO
Tyrosine (Tyr, Y)
+
H 3N
COO
Valine (Val, V)