Download - Biomolecule ชีวเคมีพื้นฐาน 1-53
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. MD 338
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Chemical levelAtoms combine toform molecules
1
2
3
4
Cellular levelCells are made up of molecules
Tissue levelTissues consist ofsimilar types of cells
5 Organ system levelOrgan systems consist of different organs that
work together closely
Organ levelOrgans are made up ofdifferent types of tissues
6 Organismal levelThe human organism ismade up of many organsystems
Atoms
MoleculesSmooth muscle cell
Smooth
muscletissue
Connectivetissue
Smoothmuscletissue
Epithelialtissue
Bloodvessel(organ)
Heart
Bloodvessels
Cardiovascularsystem
Levels of Structural Organization
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:
y Carbon (C)y Oxygen (O)
y Nitrogen (N)
y Hydrogen (H)
y
Phosphorus (P)y Sulfur (S)
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Macromolecules of Cellsy Macro = large
y 4 types of macromolecules in cellular biology
1. Carbohydrates
2. Lipids3. Nucleic Acids
4. Proteins
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Carbohydrates
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Carbohydrates
y
y y y
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Carbohydrates
y CO2 H2O glucose O2
y Cn(H2O)n, hydrate of carbon
6CO2 + 6H2O + EnergyEnergy C6H12O6 +
GlucoseGlucose
6O2
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carbohydratesy Monosaccharides
y Trioses, tetroses, pentoses, hexoses
y Oligosaccharidesy Di, tri, tetra, penta, up to 9 or 10
y Most important are the disaccharides
y Polysaccharides or glycansy Homopolysaccharides
y Heteropolysaccharides
y Complex carbohydrates
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Monosaccharides
y :y aldose or ketose
y number of carbons in chain
Structure of a simple aldose and a simple ketose
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monosaccharide
y Fish
er projection:straight chain representation
y Haworth projection:
si
mple ri
ng
i
n perspectiv
ey Conformational representation:chair and boat configurations
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Fisher projection Haworth projectionHaworth projection
Conformational representation
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Monosaccharides can form ring structures
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Cyclic Structure for Glucose
Glucose cyclic hemiacetal formed by reaction of -CHO with -OH on C5
D-glucopyranose
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Cyclic Structure for Fructose
Cyclic hemiacetal formed by reaction of C=O at C2 with -OH at C5
D-fructofuranose
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Ring Formation
y alcohol carbonyl y 5-
membered are furanosey 6-membered rings are pyranose
O O
PyranFuran
aldotetroses, aldopentoses, ketohexoses are 5-membered most aldohexoses are 6-membered
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Hawort
h
projecti
ons
y 1
y if the substituent is to the right in the Fisher projection, it will be drawn
down in the Haworth projection
(Down-Right Rule)
O O
1
23
4
5
1
23
4
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Stereoisomer
Isomer1. D-L isomer2. Enantiomer3. Optical isomer4. Epimer
5. E-F isomer
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(-OH group atthehighest
numbered asymmetric-C
atom is written to theright)
(-OH group atthehighest
numbered asymmetric-C
atom is written to the left)
CHO
OHH
HHO
OHH
OHH
CH2OH
CHO
OHH
HHO
OHH
HHO
CH2OH
D-glucose L-glucose
1
2
3
4
5
1
2
3
4
5
1. D-L isomer
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chiral carbons
y Acarbon is chiral if it has four different groups
CH2OH
H OH
CHO
CH2OH
OH H
CHO
D-glyceraldehyde L-glyceraldehyde
asymmetric-C atom
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2. Enantiomer
Enantiomer
plane of polarized li
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3. Optical isomer
Asymmetric compounds plane of polarized light
(+) dextrorotatory
(-) levorotatory
y D-glucose +52.7y D-fructose -92.4y D-galactose +80.2y L-arabinose +104.5y D-arabinose -105.0y Lactose +55.4y Sucrose +66.5y Invert sugar -19.8
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y D-glucose +52.7y D-fructose -92.4y
D-g
alactose+80
.2y L-arabinose +104.5y D-arabinose -105.0y Lactose +55.4y Sucrose +66.5y Invert sugar -19.8
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Sugars t at iff r l at a si gl car
4. Epimer
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Anomeric c-atom
The c-atom which is involved in hemiacetal or acetal formation
5. E-F isomer
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Mutarotation
38% 62%
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Oxidation Reactions of Monosaccharides
y Benedicts Reagents: Reducing Sugars
y Aldoses and ketoses give positive tests when treated with Benedicts reagent
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carbohydratesy Monosaccharides
y Trioses, tetroses, pentoses, hexoses
y Oligosaccharidesy Di, tri, tetra, penta, up to 9 or 10
y Most important are the disaccharides
y Polysaccharides or glycansy Homopolysaccharides
y Heteropolysaccharides
y Complex carbohydrates
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InvertSugar--- when sucrose in solution,
therotation changes from detrorotatory
(+66.5)to levorotatory (-19.8).So, sucrose is called InvertSugar
fructoseglucose
+
Sucrose
Also known as table sugar. Both anomeric
carbons of glucose and fructose aretied
togetherin the glycosidic linkage;thus neitherring can open, and sucrose is not a reducing sugar.
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Oxidation Reactions of sucrose
y Benedicts Reagents: Reducing Sugars
y Aldoses and ketoses give positive tests when treated with Benedicts reagent
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E-D-glucopyranosyl-F-D-fructofuranoside)
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carbohydratesy Monosaccharides
y Trioses, tetroses, pentoses, hexoses
y Oligosaccharidesy Di, tri, tetra, penta, up to 9 or 10
y Most important are the disaccharides
y Polysaccharides or glycansy Homopolysaccharides
y Heteropolysaccharides
y Complex carbohydrates
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The
P lys cch
ride
s - g r P lye
rs
Energy Storage
Starch amylose and amypectin (plant)
Inulin (plant)
Glycogen (animal)
Structural
Cellulose (plant)
Chitin (animal)
Murein or peptidoglycan (bacteria)
Glycosaminoglycans and Proteoglycans
Function
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Starch
polysaccharide
10-30% amylose
70-90% amylopectin
(depending on the source)
E(1,4)-glycosidic linkages
E(1,6)-glycosidic linkages
E(1,4
)-g
lycos
idic linka
ges
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Starch
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E-amylose
amylose helix
iodine(I2) amylosehelix
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amylopectin
amylopectin
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Polysaccharides-Starch
Qualitative Analyses
1. Amylose + I- Blue color
2. Amylopectin + I- Reddish color
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The
P lys cch
ride
s - g r P lye
rs
Energy Storage
Starch amylose and amypectin (plant)
Inulin (plant)
Glycogen (animal)
Structural
Cellulose (plant)
Chitin (animal)
Murein or peptidoglycan (bacteria)
Glycosaminoglycans and Proteoglycans
Function
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Glycogen
polysaccharide
polymer
E(1,4) E(1,6) 8 - 12
E,F-amylases
glycogen phosphorylase
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Glycogen
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The
P lys cch
ride
s - g r P lye
rs
Energy Storage
Starch amylose and amypectin (plant)
Glycogen (animal)
Structural
Cellulose (plant)
Chitin (animal)
Murein or peptidoglycan (bacteria)
Glycosaminoglycans and Proteoglycans
Function
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Cellulose polymer F-D-glucose
F-(1,4) polysaccharide
Cotton flax: 97-99% cellulose
Wood: ~ 50% cellulose
(in starch)
(in cellulose)
Structure of cellulose
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Structure ofcellulose
C
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Cellulose
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The
P lys cch
ride
s - g r P lye
rs
Energy Storage
Starch amylose and amypectin (plant)
Inulin (plant)
Glycogen (animal)
Structural
Cellulose (plant)
Chitin (animal)
Murein or peptidoglycan (bacteria)
Glycosaminoglycans and Proteoglycans
Function
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Chitiny polysaccharide
y
y polymer N-acetylglucosamine
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Linear structures ofcellulose and chitin
(2 most abundant polysaccharides)
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Lipid
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What are lipids?What are lipids?
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LipidsLipids
(acetone, chloroform, ether, benzene)
1.
2. 3.
( precursor )
4.
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1. triglycerides (fats & oils)()
2. phospholipids()
3. steroids()( precursor )
4. waxes
()
(
)
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OOH
OH
R
O
OOH
O
R
O
R
O
O
O
R
O
R
O
OR
O
MONO LYCERIDE DI LYCERIDE TRI LYCERIDE
LYCERIDES
T i l id
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O
H2C OH
HC OH
H2C OH
HO C R
HO C R
HO C R
O
O
O
H2C O C R
O
O
H2C O C R
HC O C R+
+ 3 H2O
Glycerol 3 FattyAcids Triglyceride
Triglyceride
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16-C fatty acid: CH3(CH2)14-COO-
Non-polar polar
Fatty acids
hydrocarbon carboxylic acid
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Unsaturated fatty acids
y double bond unsaturatedfatty acids
HC CH(CH2)7COOH(CH2)7H3C
1918
10
18:1,9 or(9
18:1
H3C CH2CH2CH2CH2CH2CH2CH2CH CH(CH2)7COOH
191017n
2 3 4 5 6 7 8 9 10 18[
[9, C18:1 or n-9, 18:1
C E k ti F tt A idC E k ti F tt A id
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Common EukaryoticFatty AcidsCommon EukaryoticFatty Acids
16:0 Hexadecanoic acid Palmitic acid
18:0 Octadecanoic acid Stearic acid
16:1 (7 Hexadecenoic acid Palmitoleic acid
16:1 (t trans-hexadecenoic acid
16:2 (( Hexadecadienoic acid
16:3 ((( Hexadecatrienoic acid
18:1 (9 Octadecenoic acid Oleic acid
18:2 (9,(12 Octadecadienoic acid Linoleic acid
18:3 (9,(12,(15 Octadecatrienoic acid Linolenic acid
Saturated
fatty acids
Symbol Systematic name Trivial name
Unsaturated
fatty acids
O
O
12
34
EF
K
fatty acid with a cis-(9
double bond
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Unsaturated fatty acids
yPentaenoic acid (5 double bonds)y 20:5; 5,8,11,14,17
y [3: EPA(all-cis-5,8,11,14,17-eicosapentaenoic acid)*
yHexaenoic acid (6 double bonds)y 22:6; 4,7,10,13,16,19
y [3: DHA(all-cis-4,7,10,13,16,19-docosahexaenoic acid)*
BothFAs are foundin fish oils
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Typical fish oil supplements
Allylic CH2 group
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=C
H
-C
H
-
H
C
H
-C
H
-
H
C
H
-
H
C
H
=C
H
- =C
H
-C
H
-
H
C
H
-C
H
-
H
C
H
-C
H
-
H
C
H
-
H
C
H
=C
H
-
AllylicCH2 group
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1. triglycerides (fats & oils)()
2. phospholipids()
3. steroids()( precursor )
4. waxes
(
)
(
)
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Membrane Structure
Phospholipids
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Phospholipids
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Membrane Structure
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Phosphatidic acid
In phosphatidic acid:
C3 -OH esterified Pi
O P O
O
O
H2C
CH
H2C
OCR1
O O C
O
R2
phosphatidate
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glycerophospholipids (phosphoglycerides),
Pi is in turn esterified to a polar head group (X): e.g., choline,inositol, serine, ethanolamine.
O P O
O-
O
H2C
CH
H2C
OCR1
O O C
O
R2
X
glycerophospholipid
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Phosphatidylcholine, with choline as polar headgroup.
It is a common membrane lipid.
O P O
O
O
H2C
CH
H2C
OCR1
O O C
O
R2
CH2 CH2 N CH3
CH3
CH3
+
phosphatidylcholine
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Membrane Structure
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Membrane Structure
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Membrane Structure
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Membrane Structure
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1. triglycerides (fats & oils)()
2. phospholipids()
3. steroids()( precursor )
4. waxes
(
)
()
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Membrane Structure
Cholesterol is largelyhyd
roph
obi
c.
But it has one polar group,a hydroxyl, making itamphipathic.
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STEROID NUMBERING SYSTEM
B
C D
6
80
6
8
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Cholesterol and cholesterol esters
R
usually pal itate
The hydroxyl at C-3 is hydrophilic; the rest of theolecule is hydrophobic.
Cholesterol is a precursor of
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Steroids
Cholesterol is a precursor ofSteroid Hormone
Cholesterol is a precursor of
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Cholesterol is a precursor offat soluble vitamin
VitaminACH2OH
CH3 CH3
CH3
CH3H3C
12
34
5
67
89
HO
CH2
HH
H3C
H3C CH3
CH3
CH3
O
R1
R2
HO
R3
CH3(CH2CH2CH2CH2)2CH2CH2CH2CH(CH3)2
CH3
Vitamin D Vitamin E
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1. triglycerides (fats & oils)()
2. phospholipids()
3. steroids()( precursor )
4. waxes(
)
()
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Waxes
y
y
H3C (CH2)14 C
O
O CH2 (CH2)28-CH3
l c ai alc l
att aci
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Bees wax
Spermaceti source
Carnauba wax source
contains cetyl palmitate (from whale oil)
useful forpharmaceuticals (creams;tableting
and granulation)
from a palm tree from brazil a
hard wax used on cars and boats
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Waxes
(CH2)14H3C CH2-OH cetyl alcohol
(CH2)24H3C CH2-OH hexacosanol
(CH2)28H3C CH2-OH triacontanol (myricyl alcohol)
Examples oflong chain monohydric alcohols found inwaxes
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amino acid and protein
Amino acid
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Amino acid
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20 Standard amino acids
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20 amino acids
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9 (essential amino acids)11 (non-essential aminoacids)
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(polarity) R gro
1. Non-polar()2. Polar()3. Charged ()
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Non-Polar
Polar
charged
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1. Aliphatic : Gly, Ala, Val, Leu, Ile
2. Aromatic : Trp, Phe, Tyr3. Sulphur : Met, Cys4. Hydroxyl : Ser, Thr, Tyr5. Cyclic : Pro
6. Carboxyl : Asp, Glu7. Amine : Lys, Arg, His8. Amide : Asn, Gln
R group
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Peptide
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4
1.(Primary
structure)
2.(Secondarystructure)
3.(Tertiary structure)4.(Quaternary
structure)
(Primary
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(Primarystructure)
N-terminus
C-terminus
MAPWMHLLTVLALLALWGPNSVQAYSSQHL
CGSNLVEALYMTCGRSGFYRPHDRRELEDLQ
VEQAELGLEAGGLQPSALEMILQKRGIVDQCCNNICTFNQLQNYCNVP
Insulin protein sequence :
(Secondary
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ystructure)
(fold)
2
1. Ehelix2. Fpleated sheet
E - helix
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NH3 H-bond COOH 4
1
F-pleatedh t
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sheet
H 2
(parallel) (antiparallel)
(Tertiarystructure)
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(folding)
domain
domain folds
(Quaternarystructure)
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structure)
(subunit)
Hemoglobin tetramer
Chicken triose phosphate isomerase HIV-1 aspartic protease
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Nucl ic ci
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Nucleic Acids
y Nucleotides: y nucleotide
y (1) phosphate molecule,
y (2) nitrogenous base, and
y (3) 5-carbon sugar
y :y DNA: deoxyribonucleic acid
y , double stranded helixy
RNA: ribonucleic acidy , single stranded
y ATP: adenosine triphosphate
y
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RNA DNARNA DNA
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BaseBase
PurinePurine PyrimidinePyrimidine
PurinePurine nucleosidenucleoside
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Adenosine andAdenosine and DeoxyadenosineDeoxyadenosine
PyrimidinePyrimidine nucleosidenucleoside
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UridineUridine
CytidineCytidine
ThymidineThymidine
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Adenine nucleotideAdenine nucleotide
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Nucleotide Structure
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Nucleic Acids
y Polymer of ribofuranosiderings linked by phosphateester groups.
y Each ribose is bonded to abase.
y Ribonucleic acid (RNA)
y Deoxyribonucleic acid
(DNA)
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Structure of RNA
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Structure of DNA F-D-2-deoxyribofuranose is the sugar.
Heterocyclic bases are cytosine, thymine (insteadof uracil), adenine, and guanine.
Linked by phosphate ester groups to form the
primary structure.
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Base Pairings
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Double Helix ofDNA
y Two complementarypolynucleotide chains are
coiled into a helix.
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DNA Replication
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Additional Nucleotidesy Adenosine monophosphate (AMP), a regulatory hormone.
y Nicotinamide adenine dinucleotide (NAD), a coenzyme.
y Adenosine triphosphate (ATP), an energy source.