Chemistry of Carbohydrates and Nucleic acids - An introduction

MSB 100: Basics of Biomedical Sciences
TOPIC:

•CARBOHYDRATE CHEMISTRY
•NUCLEIC ACID CHEMISTRY
Lecturer: Dr. G. Kattam Maiyoh

11/20/13

GKM/MSB100/LECT 02/2013

Introduction
• Carbohydrates are one of the FOUR major
classes of biological molecules.

•Carbs
•Proteins
•Lipids
•NA

• Carbohydrates are also the most abundant
biological molecules.
• Carbohydrates derive their name from the
general formula Cn(H2O)~ hydrated carbon
or hydrates of carbon
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functions
• Variety of important functions in living
systems:
– nutritional (energy storage, fuels,
metabolic intermediates)
– structural (components of nucleotides,
plant and bacterial cell walls, arthropod
exoskeletons, animal connective tissue)

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– Informational (cell surface of
eukaryotes -- molecular
recognition, cell-cell
communication)
– Osmotic pressure regulation
(bacteria)

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In molecular terms
• Carbohydrates are carbon
compounds that contain large
quantities of hydroxyl groups.

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In chemical terms
Carbohydrates are chemically
characterized as:
• Poly hydroxy aldehydes or
• Poly hydroxy ketones.

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Aldoses vs Ketoses
• Sugars that contain an aldehyde group are
called Aldoses.
• Sugars that contain a keto group are called
Ketoses.

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classification
All carbohydrates can be classified as
either:
– Monosaccharides
– Disaccharides
– Oligosaccharides
– Polysaccharides.

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• Monosaccharides - one unit of carbohydrate
• Disaccharides - Two units of carbohydrates.
• Anywhere from three to ten monosaccharide
units, make up an oligosaccharide.
• Polysaccharides are much larger, containing
hundreds of monosaccharide units.

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Complexes
• Carbohydrates also can combine with lipids
to form glycolipids
OR
• With proteins to form glycoproteins /
proteoglycans.

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Isomers
• Isomers are molecules that have the same
molecular formula, but have a different
arrangement of the atoms in space.
(different structures).
• For example, a molecule with the formula
AB2C2, has two ways it can be drawn:

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Isomer 1

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Isomer 2

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Examples of isomers:
1.
2.
3.
4.

Glucose
Fructose
Galactose
Mannose

Same chemical formula C6 H12 O6

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EPIMERS
• EPIMERS are sugars that differ in
configuration at ONLY 1 POSITION.

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• Examples of epimers :
– D-glucose & D-galactose (epimeric at
C4)
– D-glucose & D-mannose (epimeric at C2)
– D-idose & L-glucose (epimeric at C5)

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Epimer set 1

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Epimer set 2

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ENANTIOMERS
Non-Superimposable COMPLETE
mirror image (differ in configuration
at EVERY CHIRAL CENTER.

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Features of Enantiomers
The two members of the pair are
designated as D and L forms.
In D form the OH group on the asymmetric
carbon is on the right.
In L form the OH group is on the left side.
For e.g: D-glucose and L-glucose are
enantiomers:
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A pair enantiomers are mirror images of each other
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Asymmetric carbon in sugars
• A carbon linked to four different atoms or
groups farthest from the carbonyl carbon
• Also called Chiral carbon

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Cyclization of sugars
• Less then 1%of CHO exist in an open chain
form (AKA: straight chain, fischer projection,
linear form)
• Predominantly found in ring form (AKA: Close,
cyclic, Haworth)
• For 6 Carbon sugars, involves reaction of C-5
OH group with the C-1 aldehyde group or C-2 of
keto group (carbonyl carbon).
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Ring forms
• Basically 2 types
• Six membered ring structures are called
Pyranoses .

Pyran ring

• Five membered ring structures are called
Furanoses .
Furan ring

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Anomeric carbon
• The carbonyl carbon after cyclization
becomes the anomeric carbon.
• This creates α and β configuration.

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• Such α and β configuration are called
diastereomers and they are not mirror images.
Enzymes can distinguished between these two
forms:
• Glycogen is synthesized from α-D
glucopyranose
• Cellulose is synthesized from β -D
glucopyranose
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MUTAROTATION
• Unlike the other stereoisomeric forms, α
and β anomers spontaneously
interconvert in solution.
• This is called mutarotation.

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Optical Activity
• When a plane polarized light is passed through a
solution containing monosaccharides the light will
either be rotated towards right or left.
• This rotation is because of the presence of
asymmetric carbon atom.
• If it is rotated towards left- levorotatory (-) (L)
• If it is rotated towards right- dextrorotatory (+) (D)
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Reducing sugar
• Sugars in which the oxygen of the
anomeric carbon is free and not attached
to any other structure, such sugars can act
as reducing agents and are called
reducing sugars.

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Polysaccharides
2 types:
– HOMOpolysaccharides (all 1 type of monomer), e.g.,
glycogen, starch, cellulose, chitin
– HETEROpolysaccharides (different types of
monomers), e.g., peptidoglycans, glycosaminoglycans

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Functions of polysaccharides:
– Glucose storage (glycogen in animals &
bacteria, starch in plants)
– Structure (cellulose, chitin, peptidoglycans,
glycosaminoglycans
– Information (cell surface oligo- and
polysaccharides, on proteins/glycoproteins and
on lipids/glycolipids)
– Osmotic regulation

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Key examples of polysaccs;

• Starch and glycogen
– Function: glucose storage

Starch -- 2 forms:
• amylose: linear polymer of a(1-> 4) linked
glucose residues
• amylopectin: branched polymer of a(1-> 4)
linked glucose residues with a(1-> 6) linked
branches

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– Glycogen:
• branched polymer of a(1-> 4) linked glucose
residues with a(1-> 6) linked branches
• like amylopectin but even more highly branched
and more compact
• branches increase H2O-solubility
– Branched structures: many nonreducing ends, but
only ONE REDUCING END (only 1 free anomeric C,
not tied up in glycosidic bond)

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• Each molecule, including all the branches,
has only ONE free anomeric C
– single free anomeric C = "reducing end" of polymer

– the only end capable of equilibrating with
straight chain form of its sugar residue, which
has free carbonyl C.

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Which can then:
– REDUCE (be oxidized by) an oxidizing
agent like Cu2+

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• Cellulose and chitin
– Function: STRUCTURAL, rigidity important
Cellulose:
• Homopolymer, b(1-> 4) linked glucose residues
• Cell walls of plants

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Chitin:

• Homopolymer, b(1-> 4) linked Nacetylglucosamine residues
• hard exoskeletons (shells) of
arthropods (e.g., insects, lobsters and
crabs)

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Nucleic acids
• Nucleic acids are polymeric macromolecules, or
large biological molecules, essential for all known
forms of life.
• Nucleic acids, which include DNA (deoxyribonucleic
acid) and RNA (ribonucleic acid), are made from
monomers known as nucleotides.
• Each nucleotide has three components: a 5-carbon
sugar, a phosphate group, and a nitrogenous
base.
• If the sugar is deoxyribose, the polymer is DNA.
• If the sugar is ribose, the polymer is RNA.
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Nucleic Acids
DNA –deoxyribonucleic acid
– Polymer of deoxyribonucleotide
triphosphate (dNTP)
– 4 types of dNTP (ATP, CTP, TTP, GTP)
NB: All made of a base + sugar +
triphosphate
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RNA –ribonucleic acid
– Polymer of ribonucleotide triphosphates
(NTP)
– 4 types of NTP (ATP, CTP, UTP, GTP)
NB: All made of a base + sugar + triphosphate
So what’s the difference?
• The sugar (ribose vs. deoxyribose) and one base
(UTP vs. TTP)

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Deoxyribose (like ribose) is a sugar with 5 carbon atoms
in a ring
Oxygen is one of the ring members
In Deoxyribose, one of the OH groups is missing and
replaced with hydrogen, Thus deoxy = - 1 oxygen
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Phosphate groups are important
because they link the sugar on one
nucleotide onto the phosphate of
the next nucleotide to make a
polynucleotide.

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Base - pairing

• Nitrogenous bases
• In DNA the four bases are:
–
–
–
–

Thymine
Adenine
Cytosine
Guanine

• In RNA the four bases are:
–
–
–
–

Uracil
Adenine
Cytosine
Guanine

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DNA and RNA are polynucleotides
• Both DNA and RNA are polynucleotides.
• They are made up of smaller molecules
called nucleotides. Nucleotide
• DNA is made of two polynucleotide strands:

Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide


• RNA is made of a single polynucleotide strand:
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DNA

•Information for all proteins stored in DNA
in the form of chromosomes or plasmids.
•Chromosomes (both circular and linear)
consist of two strands of DNA wrapped
together in a left handed helix.(imagine
screwing inwards)
•The strands of the helix are held together
by hydrogen bonds between the individual
bases.
•The “outside” of the helix consists of
sugar and phosphate groups, giving the
DNA molecule a negative charge.

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BASES

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The Rule: Complimentarity
• Adenine always base pairs with Thymine
(or Uracil if RNA)
• Cytosine always base pairs with Guanine.
• This is because there is only exactly enough room for
one purine and one pyrimidine base between the two
polynucleotide strands of DNA/RNA (see next slide).
• These bases are said to be complimentary to each other
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Complimentary Base Pairs

A-T Base pairing

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G-C Base Pairing

DNA Structure
– The DNA helix is “anti-parallel”
– Each strand of the helix
has a 5’ (5 prime) end and
a 3’ (3 prime) end.

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Central Dogma
• Replication
– DNA making a copy of itself
• Making a replica

• Transcription
– DNA being made into RNA
• Still in nucleotide language

• Translation
– RNA being made into protein
• Change to amino acid language
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Replication
• Remember that DNA is self complementary
• Replication is semiconservative
– One strand goes to next generation
– Other is new

• Each strand is a template for the other
– If one strand is 5’ AGCT 3’
– Other is:
3’ TCGA 5’
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Replica – Learning check
• Write the strand complementary to:

3’ ACTAGCCTAAGTCG 5’
Answer
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Similarity between replication and
transcription
• Both processes use DNA as the template.
• Phosphodiester bonds are formed in both
cases.
• Both synthesis directions are from 5´ to 3´.

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Differences between replication and
transcription
replication

transcription

template

double strands

single strand

substrate

dNTP

NTP

primer

yes

no

Enzyme

DNA polymerase

RNA polymerase

product

dsDNA

ssRNA

base pair

A-T, G-C

A-U, T-A, G-C

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Ribonucleic acid (RNA)
• Almost all single stranded (exception is RNAi).
• In some RNA molecules (tRNA) many of the
bases are modified (e.g. psudouridine).
• Has capacity for enzymatic function -ribozymes
• One school of thought holds that early
organisms were based on RNA instead of DNA
(RNA world).
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RNA
• Several different “types” which reflect
different functions
– mRNA (messenger RNA)
– tRNA (transfer RNA)
– rRNA (ribosomal RNA)
– snRNA (small nuclear RNA)
– RNAi (RNA interference)
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RNA function
• mRNA – transfers information from DNA to
ribosome (site where proteins are made)
• tRNA – “decodes” genetic code in mRNA,
inserts correct A.A. in response to genetic
code.
• rRNA-structural component of ribosome
• snRNA-involved in processing of mRNA
• RNAi-double stranded RNA, may be
component of antiviral defense mechanism.
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