Chem A225 Notes
Page 143
Chapter 24: Carbohydrates and Nucleic Acids
I. Introduction
A. Definitions and Naming Conventions
•
Carbohydrate: a sugar. A polyhydroxy aldehyde or ketone with the molecular formula
CnH2nOn, or any compound that can be hydrolyzed to this formula.
•
The names of sugar usually end in -ose.
•
Aldehyde or ketone:
1) Aldose: a sugar that contains an aldehyde.
2) Ketose: a sugar that contains a ketone.
•
Number of carbons:
1) Triose: a three carbon sugar
2) Tetrose: a four carbon sugar.
3) Pentose: a five carbon sugar.
4) Hexose: a six carbon sugar.
•
Saccharide: another name for a sugar.
1) Monosaccharide: a compound that contains a single sugar.
2) Disaccharide: a compound that contains two sugars connected by a covalent bond.
3) Polysaccharide: a compound that contains many sugars connected by covalent
bonds.
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
B. The Family of D-Aldoses
CHO
H
OH
CH2OH
D-(+)-glyceraldehyde
CHO
CHO
H
OH
HO
H
OH
H
D-(–)-erythrose
D-(–)-threose
CHO
HO
H
OH
H
OH
HO
H
OH
H
OH
H
H
H
CH2OH
CH2OH
D-(–)-arabinose
CHO
H
HO
H
H
HO
H
OH
HO
H
OH
H
OH
HO
H
OH
H
OH
H
OH
H
OH
HO
H
OH
H
OH
H
OH
H
OH
H
CH2OH
D-(+)-xylose
D-(–)-lyxose
H
H
OH
HO
H
HO
H
H
OH
H
D-(+)-altrose
D-(+)-glucose
CH2OH
D-(+)-mannose
H
OH
CH2OH
D-(–)-gulose
CHO
CHO
HO
CH2OH
OH
CH2OH
OH
CH2OH
H
OH
CHO
CHO
H
D-(+)-allose
H
CHO
OH
HO
H
H
H
CHO
OH
HO
H
OH
HO
H
HO
H
H
HO
H
HO
H
OH
CH2OH
D-(–)-idose
H
OH
CH2OH
D-(+)-galactose
H
OH
CH2OH
D-(+)-talose
Page 144
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
D-(–)-ribose
CHO
CHO
OH
Ch 24: Carbohydrates and Nucleic Acids
CH2OH
H
CH2OH
OH
CH2OH
CHO
CHO
H
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 145
C. Important Sugars in Biochemistry (MEMORIZE THESE)
O
H
C
H
HO
CH 2OH
OH
H
C
HO
O
H
C
O
H
H
OH
O
H
OH
H
OH
H
OH
H
OH
H
OH
H
OH
CH2OH
CH 2OH
CH2OH
D-glucose
D-fructose
D-ribose
H
C
H
OH
CH2OH
D-glyceraldehyde
II. Monosaccharides
A. D/L Configurations and Epimers
•
Sugars are chiral and exist as pairs of non-superimposable mirror images
(enantiomers):
•
We need a convenient way of distinguishing between the two enantiomers of a sugar.
•
Use the configuration of the highest numbered stereocenter in the Fischer projection of
the sugar (look at atom C-5 in the above structures).
•
Look at the configuration of the highest priority (by R/S rules) group (usually OH or
NH) on the highest numbered stereocenter in the Fischer projection:
•
On the right side of the projection = D enantiomer
•
On the left side of the projection = L enantiomer
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
•
Ch 24: Carbohydrates and Nucleic Acids
Page 146
Examples: Classify the following as D or L enantiomers:
CHO
CHO
HO
H
HO
H
HO
HO
H
H
CH2OH
ribose
CHO
H
HO
H
OH
HO
H
CH2OH
threose
CH2OH
erythrose
CHO
H
OH
CH2OH
glyceraldehyde
•
In a pair of enantiomers, all stereocenters have the opposite configuration (all
stereocenters are mirror images).
•
Some closely related sugars differ in having only one stereocenter of opposite
configuration. These are epimers: pairs of chiral molecules that differ in the
configuration of only one stereocenter (all other stereocenters have the same
configuration).
B. Cyclic Forms of Sugars
•
Sugars contain aldehyde/ketone carbonyls and alcohol hydroxyl groups, so they can do
an intramolecular reaction to make a hemiacetal (review section 20.5, pp. 923–931).
•
Cyclic forms of sugars are called furanose or pyranose, depending on if they have a
five- or six-membered ring:
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 147
•
Haworth Projection: draw the cyclic form as a flat ring with groups straight up and
down.
•
Rules for Converting Fischer projections to Haworth projections:
1) Identify the carbon with the OH that forms the ring.
Count the atoms in the ring, and draw the ring skeleton.
Put the ring oxygen in back, and carbon 1 on the right.
2) Write all the groups except the tail and C1 onto the ring.
•
Groups on right of Fischer = down on Haworth
•
Groups on left of Fischer = up on Haworth
3) Direction of tail depends on direction of the OH that
formed the ring:
•
Ring forming OH on right = tail up
•
Ring forming OH on left = tail down
4) The hemiacetal carbon can have the OH up or down.
•
OH is cis to the tail = β stereoisomer
•
OH is trans to the tail = α stereoisomer
If the stereochemistry is not specified, a wavy bond can
be written.
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
•
Ch 24: Carbohydrates and Nucleic Acids
Page 148
The pyranose (6-membered ring) forms of sugars can also be written as chairs:
C. Mutarotation and Anomers
•
Most carbohydrates are chiral compounds, so they rotate plane-polarized light.
Recall that the direction and magnitude (angle) of rotation (at a given concentration,
cell length, and wavelength) is a physical constant called the specific rotation and
symbolized as [α]D.
•
D-glucose is unusual because it has two different values for [α] depending on the
conditions under which it is crystallized:
•
Low temperature crystals: mp = 146 oC, [α]D = +112o
•
High temperature crystals: mp = 150 oC, [α]D = +19o
•
Furthermore, when either type of crystal is dissolved in water, the initial rotation
gradually changes until it reaches a constant value of +52.7o. This is called
mutarotation (muta is a prefix meaning change).
•
There are two forms of D-glucopyranose (the cyclic hemiacetal form of D-glucose).
They differ in the configuration of the OH that is formed at C1:
CHO
H
HOCH2
O
HO
HO
HO
H
HO
OH
OH
H
H
OH
H
OH
HOCH2
O
HO
HO
OH
HO
H
CH2OH
α-D-glucopyranose
D-glucose
β-D-glucopyranose
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 149
•
These two different forms of glucopyranose are called anomers, and the carbon that
changes configuration is called the anomeric carbon.
•
As shown above, the anomeric pyranose forms are in equilibrium with the open form
of glucose. This means that each molecule of glucose is rapidly forming a ring and
then re-opening.
•
When the alpha (α) form of glucopyranose opens, the open-chain glucose can either
reclose in the alpha form, or it can close in the beta form. Thus, over time a sample of
100% α-D-glucopyranose will change to a mixture of the alpha and the beta form.
•
Thus, the two crystal forms isolated are the 100% pure anomers. The alpha anomer has
a specific rotation of +112o. When either form is dissolved in water, they gradually
equilibrate to a mixture of 36% alpha and 64% beta, which has a rotation in between
the rotations of the two pure anomers:
% alpha form
% beta form
[α]D
Low Temp Crystal
100%
0%
+112o
High Temp Crystal
0%
100%
+19o
Equilibrium mixture
36%
64%
+52.6o
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 150
D. Glycoside Formation
•
Observed reaction:
•
Mechanism (review acetal formation)
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 151
•
Glycosides can be hydrolyzed in aqueous acid:
•
Glycosides are named by naming the alkyl group of the ROH (alcohol), and changing
the -ose ending of the carbohydrate name to -oside.
III.Polysaccharides (Oligomers of Carbohydrates)
•
Oligomer: a molecule constructed from two or more smaller molecules.
•
Monomer: a small molecule that can be connected to other monomers to build up an
oligomer.
A. Sugars can be connected by forming glycosides:
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 152
B. Sucrose (a disaccharide)
HOCH 2
H
O
HOCH 2
OH
O
HO
OH
HO
HO
α-D-glucopyranose
HO
HOCH 2
HOCH 2
HO
O
HO
H
H
OH
O
O
HO
H
CH2OH
CH2OH
OH
OH
sucrose
β-D-f ructof uranose
C. Starch (a polysaccharide)
HOCH2
3
O
4
O
HO
3
HO
2
H
1
O
HOCH2
HO
•
O
4'
2'
3' HO
1' H
O
Starch is used to store glucose in plants for later use. Why?
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 153
D. Glycogen (a polysaccharide)
HOCH2
O
O 4
HO
3 HO
H
2
1
HOCH 2
O
O
HO
H
HO
1
HOCH 2
O
O
O 4
HO
3 HO
H
2
6' CH
1
2
O
HO
•
O
4'
1' H
2'
3' HO
O
Glycogen is used to store glucose in higher organisms (like mammals). Why?
E. Cellulose (a polysaccharide)
HOCH2
4
HOCH 2
O
O
HO
3 HO
2
O
1
H
4'
HO
2'
3' HO
O
1' O
H
•
Used as a structural compound in plants (cell wall, wood, fiber, cotton).
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 154
IV.Nucleic Acids: DNA and RNA
A. Introduction
•
Nucleic acids: acidic compounds found in the nucleus of cells. Nucleic acids carry the
genetic information of the cell.
•
Two main types of nucleic acids:
•
Ribonucleic acids (RNA): used mainly for transfer of genetic information to build
proteins. Also catalyzes chemical reactions in protein synthesis and stores genetic
information in some viruses.
•
Deoxyribonucleic acids (DNA): used for long-term storage of genetic
information.
B. Nucleosides and Nucleotides: Building Blocks of Nucleic Acids
•
RNA and DNA have a chain of sugars connected by phosphates (the sugar-phosphate
backbone). Example: RNA backbone:
5' end
O
5' end
O-
P
O
O
O
CH2
H
H
O
H
O
HO
O
O
H
O
HO
O
H
H
O
O
base2
O
O
CH2
O-
Ribose
H
O-
P
P
O
base2
O
H
H
base1
O
O
CH2
O-
Ribose
H
O-
P
P
O
base1
O
O
base3
O-
O
H
HO
P
Ribose
H
base3
3' end
3' end
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 155
•
In RNA, the sugar is ribose. In DNA, the sugar is 2-deoxyribose (removing the
hydroxyl group at carbon 2 makes the DNA chain more stable).
•
The sugars have cyclic amine bases (purines and pyrimidines) attached at the anomeric
carbon (the hemiacetal carbon of the furanose form of the sugar).
NH2
N
N
N
N
H
N
N
O
O
H
N
O
H
pyrimidine
NH2
guanine (G)
N
N
N
H
NH2
N
N
N
N
adenine (A)
N
H
N
N
H
purine
O
cytosine (C)
N
O
CH3
H
N
N
O
H
H
uracil (U)
thymine (T)
•
Most of the bases are the same, except that RNA uses uracil (U) where DNA uses
thymine (T), which has an extra methyl group. The extra methyl group helps make
DNA more stable than RNA (so it has better long-term stability).
•
Notice that some of the bases exist in the keto forms of tautomer. The enol forms
would be aromatic according to Huckel’s rules:
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
•
Ch 24: Carbohydrates and Nucleic Acids
Page 156
The sugar and base together is called a nucleoside. When the nucleoside has a
phosphate attached to the C-5 hydroxyl, the entire molecule is called a nucleotide.
NH2
N
HO
CH2
N
O
H
H
OH
H
OH
H
N
N
HO
N
CH2
H
H
OH
H
OH
H
adenosine (A)
O
-
O
O
NH2
-
O
O
N
N
H
H
OH
H
OH
H
O
N
CH2 O
N
H
H
OH
H
OH
H
N
H
N
O
N
OH
HO
CH2
H
deoxyadenosine
N
O
P
H
H
OH
H
OH
OH
H
deoxyguanosine
H
OH
O
O-
P
NH
CH2
O
cytidine monophosphate,
CMP (cytidylic acid)
N
O
H
H
OH
H
OH
O
CH3
N
NH2
HO
CH2
N
O
H
OH
O
HO
CH2
H
H
H
deoxycytidine
O
uridine monophosphate,
UMP (uridylic acid)
NH2
H
H
OH
H
NH
N
H
O
O
N
O
H
O
-O
O
CH2
NH2
N
O
uridine (U)
NH2
H
H
CH2
H
-
H
N
H
H
OH
H
OH
O
H
H
H
HO
O
guanosine monophosphate,
GMP (guanidylic acid)
N
N
H
O
N
NH
N
N
O
O
-
O
NH
cytidine (C)
O
NH2
CH2
CH2
H
O
adenosine monophosphate,
AMP (adenylic acid)
HO
HO
NH2
-
P
N
O
CH2 O
N
guanosine (G)
-
P
N
NH
N
O
O
NH2
O
NH
N
O
H
H
OH
H
H
O
H
deoxythymidine
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 157
C. Structure of Nucleic Acid Chain
•
The chains of nucleic acids are built of alternating sugar-phosphate units (for example,
the backbone of RNA):
5' end
5' end
OH
O-
P
O
OH
O
O
CH2
base1
O
H
H
CH2
H
OH
HO
H
H
O
OH
O
O-
P
H
H
H
H
O
HO
OH
O
H
O-
P
CH2
CH2
base1
O
O
O
3' end
O-
P
O
base2
H
H
H
HO
H
3' end
OH
O
base2
H
HO
H
•
The sugars are connected as esters of phosphoric acid (phosphate esters).
•
The connection is from the 3’-hydroxyl to the phosphate to the 5’-hydroxyl of another
sugar.
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 158
D. Base Pairing in RNA and DNA
•
The amine bases of nucleic acids and nucleosides can form hydrogen bonds with each
other.
H
O
N
N
ribose
N
H
H
N
N
N
H
N
ribose
N
N
H
N
N
O
H
H
N
O
N
N
N
ribose
O
ribose
H
guanine
•
G:::C
cytosine
A::T
thymine
Guanine bonds with cytosine (G-C), while adenine bonds with thymine (A-T) in DNA
or uracil (A-U) in RNA.
O-
3' end
HO
ribose
O
T
O
HO
5' end
P
O-
O
ribose
P
OO
O
A
•
adenine
P
O-
O
G
O
ribose
P
O
O
C
O
O
ribose
P
O-
O
5' end
P
OH
O
G
C
O
O
ribose
O-
O
ribose
OH
3' end
The G-C pair has three hydrogen bonds, while the A-T pair has only two hydrogen
bonds. A greater amount of G-C in a strand of DNA makes it more stable.
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
Ch 24: Carbohydrates and Nucleic Acids
Page 159
E. Double Helix of DNA
•
Bases of one chain of DNA will pair up with bases on a complementary chain of DNA,
forming two intertwined chains. The chains twist into a helix as they pair. Because
there are two chains, this is called a double helix.
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.
Chem A225 Notes
•
Ch 24: Carbohydrates and Nucleic Acids
Page 160
A complementary copy of a DNA chain can by made by pairing up complementary
nucleotides, then connecting the nucleotides into a chain with a DNA polymerase
enzyme.
Lecture Notes © 2017 Dr. Thomas Mucciaro. All rights reserved.