How to Troubleshoot Apps for the Modern Connected Worker
Chemistry of Carbohydrates and Nucleic acids - An introduction
1. 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
2. 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
11/20/13
GKM/MSB100/LECT 02/2013
3. 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)
11/20/13
GKM/MSB100/LECT 02/2013
5. In molecular terms
• Carbohydrates are carbon
compounds that contain large
quantities of hydroxyl groups.
11/20/13
GKM/MSB100/LECT 02/2013
6. In chemical terms
Carbohydrates are chemically
characterized as:
• Poly hydroxy aldehydes or
• Poly hydroxy ketones.
11/20/13
GKM/MSB100/LECT 02/2013
7. Aldoses vs Ketoses
• Sugars that contain an aldehyde group are
called Aldoses.
• Sugars that contain a keto group are called
Ketoses.
11/20/13
GKM/MSB100/LECT 02/2013
9. classification
All carbohydrates can be classified as
either:
– Monosaccharides
– Disaccharides
– Oligosaccharides
– Polysaccharides.
11/20/13
GKM/MSB100/LECT 02/2013
10. • 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.
11/20/13
GKM/MSB100/LECT 02/2013
11. Complexes
• Carbohydrates also can combine with lipids
to form glycolipids
OR
• With proteins to form glycoproteins /
proteoglycans.
11/20/13
GKM/MSB100/LECT 02/2013
12. 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:
11/20/13
GKM/MSB100/LECT 02/2013
23. 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:
11/20/13
GKM/MSB100/LECT 02/2013
24. A pair enantiomers are mirror images of each other
11/20/13
GKM/MSB100/LECT 02/2013
28. Asymmetric carbon in sugars
• A carbon linked to four different atoms or
groups farthest from the carbonyl carbon
• Also called Chiral carbon
11/20/13
GKM/MSB100/LECT 02/2013
30. 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).
11/20/13
GKM/MSB100/LECT 02/2013
31. Ring forms
• Basically 2 types
• Six membered ring structures are called
Pyranoses .
Pyran ring
• Five membered ring structures are called
Furanoses .
Furan ring
11/20/13
GKM/MSB100/LECT 02/2013
33. Anomeric carbon
• The carbonyl carbon after cyclization
becomes the anomeric carbon.
• This creates α and β configuration.
11/20/13
GKM/MSB100/LECT 02/2013
35. • 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
11/20/13
GKM/MSB100/LECT 02/2013
36. MUTAROTATION
• Unlike the other stereoisomeric forms, α
and β anomers spontaneously
interconvert in solution.
• This is called mutarotation.
11/20/13
GKM/MSB100/LECT 02/2013
39. 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)
11/20/13
GKM/MSB100/LECT 02/2013
40. 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.
11/20/13
GKM/MSB100/LECT 02/2013
41. Polysaccharides
2 types:
– HOMOpolysaccharides (all 1 type of monomer), e.g.,
glycogen, starch, cellulose, chitin
– HETEROpolysaccharides (different types of
monomers), e.g., peptidoglycans, glycosaminoglycans
11/20/13
GKM/MSB100/LECT 02/2013
42. 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
11/20/13
GKM/MSB100/LECT 02/2013
43. 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
11/20/13
GKM/MSB100/LECT 02/2013
44. – 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)
11/20/13
GKM/MSB100/LECT 02/2013
45. • 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.
11/20/13
GKM/MSB100/LECT 02/2013
46. Which can then:
– REDUCE (be oxidized by) an oxidizing
agent like Cu2+
11/20/13
GKM/MSB100/LECT 02/2013
48. • Cellulose and chitin
– Function: STRUCTURAL, rigidity important
Cellulose:
• Homopolymer, b(1-> 4) linked glucose residues
• Cell walls of plants
11/20/13
GKM/MSB100/LECT 02/2013
49. Chitin:
• Homopolymer, b(1-> 4) linked Nacetylglucosamine residues
• hard exoskeletons (shells) of
arthropods (e.g., insects, lobsters and
crabs)
11/20/13
GKM/MSB100/LECT 02/2013
50. 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.
11/20/13
GKM/MSB100/LECT 02/2013
51. 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
11/20/13
GKM/MSB100/LECT 02/2013
52. 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)
11/20/13
GKM/MSB100/LECT 02/2013
54. Phosphate groups are important
because they link the sugar on one
nucleotide onto the phosphate of
the next nucleotide to make a
polynucleotide.
11/20/13
GKM/MSB100/LECT 02/2013
55. Base - pairing
• Nitrogenous bases
• In DNA the four bases are:
–
–
–
–
Thymine
Adenine
Cytosine
Guanine
• In RNA the four bases are:
–
–
–
–
Uracil
Adenine
Cytosine
Guanine
11/20/13
GKM/MSB100/LECT 02/2013
56. 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
Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide
Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide
• RNA is made of a single polynucleotide strand:
11/20/13
GKM/MSB100/LECT 02/2013
57. 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.
11/20/13
GKM/MSB100/LECT 02/2013
59. 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
11/20/13
GKM/MSB100/LECT 02/2013
61. 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.
11/20/13
GKM/MSB100/LECT 02/2013
63. 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
11/20/13
GKM/MSB100/LECT 02/2013
64. 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’
11/20/13
GKM/MSB100/LECT 02/2013
65. Replica – Learning check
• Write the strand complementary to:
3’ ACTAGCCTAAGTCG 5’
Answer
11/20/13
GKM/MSB100/LECT 02/2013
66. 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´.
11/20/13
GKM/MSB100/LECT 02/2013
67. 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
11/20/13
GKM/MSB100/LECT 02/2013
68. 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).
11/20/13
GKM/MSB100/LECT 02/2013
69. RNA
• Several different “types” which reflect
different functions
– mRNA (messenger RNA)
– tRNA (transfer RNA)
– rRNA (ribosomal RNA)
– snRNA (small nuclear RNA)
– RNAi (RNA interference)
11/20/13
GKM/MSB100/LECT 02/2013
70. 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.
11/20/13
GKM/MSB100/LECT 02/2013