biomolecule ชีวเคมีพื้นฐาน 1-53

8/7/2019 Biomolecule 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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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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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


Inulin (plant)

Glycogen (animal)

Structural

Cellulose (plant)

Chitin (animal)



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


Glycogen (animal)

Structural

Cellulose (plant)

Chitin (animal)



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


Inulin (plant)

Glycogen (animal)

Structural

Cellulose (plant)

Chitin (animal)



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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2. phospholipids()


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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2. phospholipids()


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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2. phospholipids()


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.

biomolecule ชีวเคมีพื้นฐาน 1-53

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