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PHYS 4xx Intro 2
1
PHYS 4xx Intro 2 - Molecular building blocks
We now describe in more detail the nomenclature and composition of several classes of
compounds of relevance to the cell, including:
membrane components: fatty acids and phospholipids
biopolymers: sugars, amino acids and proteins
the genetic blueprint: DNA and RNA.
Fatty acids and phospholipids
Phospholipids contain two fatty acids linked to a glycerol backbone. The remaining OH
group in the glycerol is replaced by a phosphate group PO4 that is linked a the polar
head group:
O
O
O
PO 4
O
Head
group
The polar head groups of phospholipids may be chosen from a variety of organic
compounds, including
NH3 +
CH3 CH3 CH3
choline
CH2 OH
OH
COO-
NH3 +
N+
CH2
CH
CH
CH2
CH2
CH2
CH2
CH2
ethanolamine
glycerol
serine
Because PO4 has a negative charge, serine and glycerol phospholipids are negative
while choline and ethanolamine phospholipids are neutral.
The naming convention for a phospholipid mirrors, in part, its fatty acid composition.
Common abbreviations (italics provided for ease of pronounciation) include:
phosphatidylcholine
phosphatidylglycerol
PC
PG
phosphatidylethanolamine
phosphatidylserine
PE
PS.
2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited.
PHYS 4xx Intro 2
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Some fatty acids commonly found in membrane lipids
__________________________________________________________________
Acid name
Total number of
Number of
Position of
carbon atoms
double bonds
double bond
__________________________________________________________________
lauric
12
0
myristic
14
0
palmitic
16
0
palmitoleic
16
1
9-cis
stearic
18
0
oleic
18
1
9-cis
linoleic
18
2
9-cis, 12-cis
arachidonic
20
4
9-cis, 8-cis, 11-cis, 14-cis
__________________________________________________________________
Column 4 displays the C-C bond numbers on which any double bonds occur.
Not all phospholipids are based solely on fatty acids. For example, sphingomyelin
OH
CH
CH
NH
CH2
PO 4
CH2 CH2 N+ (CH3 )3
O
Some lipids present in cellular membranes are not phospholipids:
sugar
cholesterol
OH O
glycolipid
HO
NH
O
Sugars
Sugar molecules are one component of DNA and of the peptidoglycan network of the
bacterial cell wall. A single sugar molecule has the chemical formula (CH2O)n, the most
biologically important sugars having n = 5 or 6. Examples of the conformations
available for the glucose molecule (n = 6) are:
2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited.
PHYS 4xx Intro 2
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CH2OH
OH
HO
CH2OH
H
OH
O
O
CH2OH
OH
OH
HO
OH
OH
OH
HO
OH
(a)
O
HO
(b)
(c)
Panel (a) shows the molecule as a linear chain. Five of the oxygens are part of -OH
groups while the sixth is double-bonded as an aldehyde. The double-bonded oxygen
can be placed at one of several different positions on the chain, each corresponding to
an inequivalent, yet related, molecule. The chain can be closed into a ring using one of
the oxygens in a hydroxyl group (not the oxygen in the aldehyde group (RCOH)) as
illustrated in Panel (b). As drawn, the ring in part (b) appears planar, in spite of the lack
of in-plane double bonds such as are present in planar compounds like benzene. In
fact, the actual configuration of a glucose ring is the bent form in part (c), just as it is in
the single-bonded ring of cyclohexane. A single sugar molecule in isolation is referred
to as a monosaccharide. But sugar molecules can polymerize through reactions in
which two alcohol groups (one on each ring) combine to give a single bond between
rings, liberating H2O as a product. Two glucose molecules may combine to form the
disaccharide maltose (as shown) or longer polysaccharides.
CH2OH
CH2OH
O
O
OH
HO
O
OH
OH
OH
OH
Amino acids and proteins
Proteins are linear chains of amino acids, a family of organic compounds containing an
amino group (-NH3+) and a carboxyl group (-COO-). Amino acids can join together to
form chains through an amide linkage (-OC-N-) referred to as a peptide bond. The
reaction liberates H2O, and has the general form:
H
H
N C
H
R1
O
H
+
C
OH
R2
N C
H
H
O
H2 O
H
C
H
N C
OH
H
R1
O
R2
C N
C C
H
H
O
OH
peptide
bond
The side groups R1 and R2 are chosen from only 20 different residues in protein
construction, none of which has a high molecular mass:
2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited.
PHYS 4xx Intro 2
CH3
alanine
4
CH2
CH2
CH2
C
NH
arginine
C
+
NH2
CH
CH3 CH2
C
HN
CH3
NH+ isoleucine
HC
histidine
COO
HN
-
CH2
CH2
CH2
SH
O cysteine
O
C
aspartic
O
Oacid
glutamic
acid
C
-
CH2
C
NH2
O
glutamine
NH2
CH2
H
glycine
NH2
O
asparagine
CH2
CH2
CH2
CH
CH2
CH
CH3 CH3
leucine
CH2
CH2
CH2
CH2
CH2
CH3 S
methionine phenylalanine
CH2
lysine
CH2
NH2
H
C
CH2
CH2
CH2
proline
CH2
OH
serine
CH
OH CH3
threonine
CH2
N
tryptophan H
CH2
CH
CH3 CH3
valine
tyrosine
OH
A protein chain of high molecular mass will be built up as this reaction occurs
repeatedly; for example, the two inequivalent spectrin proteins in the human erythrocyte
have molecular masses of ~220 000 and ~230 000 Da.
Amino acids appear in a protein with varying relative abundance, and some, such as
tryptophan, are uncommon.
In a large protein, the average molecular mass of the amino acids is 115 Da.
Nucleotides and DNA
Ribonucleic acid, or RNA, directs protein synthesis in the cell, whereas deoxyribonuclei
acid, or DNA, is the carrier of genetic information. The elementary chemical units of
DNA and RNA are nucleotides, which are composed of subunits, namely a sugar, an
organic base and a phosphate group.
phosphate
base
nucleotide:
sugar
2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited.
PHYS 4xx Intro 2
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The two different sugars found in nucleotides, ribose in RNA and deoxyribose in DNA,
are five-membered rings differing from each other by only one oxygen atom.
HOCH2
OH
O
H
H
H
H
OH
OH
HOCH2 O
OH
H
H
H
H
OH H
deoxyribose
ribose
In either molecule, the OH groups are potential reaction sites for addition of a base.
Five organic bases are found in nucleotides, and they fall into two chemically similar
groups - purines and pyrimidines. Only four of the five bases are present in a given
DNA or RNA molecule, and the one "missing" base is different for each:
RNA: adenine, guanine, cytosine, uracil
DNA: adenine, guanine, cytosine, thymine.
O
NH2
C
N
HN
C
CH
CH
Purines
C
C N
HC
C N
N
N
H2N
H
H
Adenine (DNA + RNA)
Guanine (DNA + RNA)
O
O
NH
N
C
C
N
2
Pyrimidines
O
C
CH
HN
C N CH
C
N
H
Cytosine (DNA + RNA)
O
C
C
CH3
N CH
H
Thymine (DNA)
HN
O
C
C N
CH
CH
H
Uracil (RNA)
The reaction of a sugar with a base releases water (an -OH from the sugar plus an H
from the base) and produces a sugar-base combination called a nucleoside. Addition of
a phosphate to a nucleoside releases water and produces a nucleotide, two of which
are shown in the chain of Panel (a). The nucleotides themselves can polymerize to
form DNA and RNA, through a linkage between a sugar from one nucleotide and a
phosphate from another, as schematically illustrated in Panel (a).
2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited.
PHYS 4xx Intro 2
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O-O P O
sugar
base
O
H2C
O
H
H
H
PO4
sugar
H
O
OH
-O P O
sugar
PO4
base
O
O
H2C
H
PO4
H
PO4
sugar
H
H
OH OH
(a)
(b)
In the double-stranded helix of DNA, the bases lie in the interior of the helix, and hold
the helix together through hydrogen bonding between base-pairs. Each matching base
pair on the opposing strands consists of one purine and one pyrimidine:
adanine/thymine and guanine/cytosine.
ADP and ATP
The energy currency of the cell is based upon a sugar-base-phosphate nucleotide
whose elementary components are the same as RNA. The sugar of the currency is
ribose of RNA, and the most common base is adenine (or, much less frequently,
guanine). The currency differs from RNA by the presence of more than one phosphate
group: the lower energy state of the pair has two phosphate groups (adenosine
diphosphate, or ADP), while the higher energy state has three (adenosine triphosphate,
or ATP).
adenine
PO4 PO4
ribose
phosphorylation
adenine
PO4 PO4 PO4
hydrolysis
ribose
The energy-consuming process of adding a phosphate is called phosphorylation, while
the release of a phosphate is hydrolysis. Depending on conditions, the energy change
for a single phosphate group is 11-13 kcal/mol, corresponding to 8 x 10-20 J = 20kBT per
reaction.
2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited.