4. nukleotida, dna,rna ok

8/11/2019 4. Nukleotida, DNA,RNA OK

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Nucleotides and nucleic acids

1

Nucleotides are the building blocks ofnucleic acids

Nucleotides also play other important roles in the cell

Nucleotide DNA RNA


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Roles of nucleotides

10/10/05 2

Building blocks of nucleic acids (RNA, DNA) Analogous to amino acid role in proteins Energy currency in cellular metabolism (ATP:

adenosine triphosphate)

Allosteric effectors Structural components of many enzymecofactors (NAD: nicotinamide adeninedinucleotide)


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Roles of nucleic acids

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DNA contains genes, the information needed tosynthesize functional proteins and RNAs DNA contains segments that play a role in regulation ogene expression (promoters)

Ribosomal RNAs (rRNAs) are components of ribosom

playing a role in protein synthesis Messenger RNAs (mRNAs) carry genetic informationfrom a gene to the ribosome

Transfer RNAs (tRNAs) translate information in mRNinto an amino acid sequence

RNAs have other functions, and can in some casesperform catalysis


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Structure of nucleotides

10/10/05 4 Fig. 8-1

A phosphate group

Nucleotides have three characteristic components

A nitrogenous base(pyrimidines or purine)

A pentose sugar


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Structure of nucleosides

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Remove the phosphate group, and you have a nucleoside .

H


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ATP is a nucleotide - energy currency

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DG = -50 kJ/mol

triphosphate Base (adenine)

Ribose sugar


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NAD is an important enzyme cofactor

10/10/05 7

Fig. 13-15

NADH is a hydride transfer agent,

or a reducing agent.Derived from Niacin

nicotinamide


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Nucleotides play roles in regulation

10/10/05 8

Fig. 6-30


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Structure of nucleotides

10/10/05 9

Below is the general structure of a nucleotide. Thepentose sugar, the base, and the phosphate moietiesall show variations among nucleotides.

Know this!


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The ribose sugar

10/10/05 10


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Ribose

10/10/05 11 Fig. 8-3

Ribose (b-D-furanose) isa pentose sugar (5-membered ring).

Note numbering of thecarbons. In a nucleotide,"prime" is used (todifferentiate from basenumbering).

5

1

2 3 4


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Ribose

10/10/05 12 Fig. 8-3

An important derivative of

ribose is 2'-deoxyribose,or just deoxyribose, inwhich the 2' OH isreplaced with H.

Deoxyribose is in DNA

(deoxyribonucleic acid) Ribose is in RNA(ribonucleic acid).

The sugar prefersdifferent puckers in DNA(C-2' endo) and RNA C-3'endo).


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The purine or pyrimidine base

10/10/05 13


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Pyrimidine and purine

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Fig. 8-1

Know these!

Nucleotide bases in nucleic acids are pyrimidines or purin


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Pyrimidine and purine

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Nucleotide bases in nucleic acids are pyrimidines or purin


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Major bases in nucleic acids

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Fig. 8-2

Among the pyrimidines, Coccurs in both RNA andDNA, but

T occurs in DNA, and U occurs in RNA

Know these!

The bases areabbreviated by their firstletters (A, G, C, T, U).

The purines (A, G) occurin both RNA and DNA


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Some minor bases

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Fig. 8-5

5-Methylcytidine occurs in DNA of animals and higher pl N 6-methyladenosine occurs in bacterial DNA

Fig. 8-5


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The phosphate

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h h


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Variation in phosphate group

10/10/05 xFig. 8-6, 8-42

Adenosine 3', 5'-cyclic

monophosphate (cyclic AMPor cAMP) is an importantregulatory nucleotide.

In hydrolysis of RNA bysome enzymes,

ribonucleoside 2',3'-cyclicmonophosphates are isolableintermediates;ribonucleoside 3'-monophosphates are endproducts Another variation - multiplephosphates (like ATP).

cAMP

19 10/10/05

l d l d


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Nucleotides in nucleic acids

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Bases attach to the C-1' of ribose or deoxyribose

The pyrimidines attach to the pentose via the N-1 position ofthe pyrimidine ring The purines attach through the N-9 position Some minor bases may have different attachments.

ib l id


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Deoxyribonucleotides

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Fig. 8-4

2'-deoxyribose sugar

Deoxyribonucleotides are abbreviated (for example) A, or

dA (deoxyA), or dAMP (deoxyadenosine monophosphate)

Phosphorylate the 5' position

and you have a nucleotide(here,deoxyadenylate ordeoxyguanylate)

with a base (here, a purine,adenine or guanine)attached to the C-1'position is adeoxyribonucleoside (here deoxyadenosine anddeoxyguanosine).

Th j d ib l id


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The major deoxyribonucleotides

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Fig. 8-4

Rib l id


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Ribonucleotides

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Fig. 8-4

The ribose sugar with abase (here, a pyrimidine,uracil or cytosine) attachedto the ribose C-1' positionis a ribonucleoside (here,uridine or cytidine).

Phosphorylate the 5'position and you have aribonucleotide (here,uridylate or cytidylate)

Ribonucleotides are abbreviated (for example) U, or UMP(uridine monophosphate)

Th j ib l id


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The major ribonucleotides

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Fig. 8-4

N l id l


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Nucleotide nomenclature

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N l id l


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Nucleotide nomenclature

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Fig. 8-39

N l i id


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Nucleic acids

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Fig. 8-7

Nucleotide monomers

can be linked together via aphosphodiester linkageformed between the 3' -OHof a nucleotide

and the phosphate of thenext nucleotide.Two ends of the resulting poly-or oligonucleotide are defined:

The 5' end lacks a nucleotide atthe 5' position,and the 3' end lacks a nucleotideat the 3' end position.

S h h t b kb


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Sugar-phosphate backbone

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Berg Fig. 1.1

The polynucleotide or nucleic acid backbone thus consists ofalternating phosphate and pentose residues.

The bases are analogous to side chains of amino acids; they vawithout changing the covalent backbone structure.

Sequence is written from the 5' to 3' end: 5'-ATGCTAGC-3' Note that the backbone is polyanionic. Phosphate groups pKa

Th b k i i i


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The bases can take syn or anti positions

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Fig. 8-18b

S h h t b kb f ti


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Sugar phosphate backbone conformation

10/10/05 30

Fig. 8-18a

Polynucleotides haveunrestricted rotation about mostbackbone bones (within limits ofsterics)

with the exception of the sugarring bond

This behavior contrasts with thepeptide backbone.

Also in contrast with proteins,specific, predictable interactionsbetween bases are often formed:A with T, and G with C.

These interactions can beinterstrand, or intrastrand.

C l l tid d l tid


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Compare polynucleotides and polypeptides

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As in proteins, the sequence of side chains(bases in nucleic acids) plays an importantrole in function.

Nucleic acid structure depends on the

sequence of basesand on the type of ribosesugar (ribose, or 2'-deoxyribose). Hydrogen bonding interactions are

especially important in nucleic acids.

I t t d H b di g b t DNA b


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Interstrand H-bonding between DNA bases

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Fig. 8-11

Watson-Crick base pairing

DNA t t d t i ti


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DNA structure determination

10/10/05 33

Franklin collected x-raydiffraction data (early 1950s)that indicated 2 periodicitiesfor DNA: 3.4 and 34 .

Watson and Crick proposed a 3-D model accounting for the data.

DNA t t


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DNA structure

10/10/05 34

Fig. 8-15

DNA consists of two helicalchains wound around thesame axis in a right-handedfashion aligned in anantiparallel fashion.

There are 10.5 base pairs, or

36 , per turn of the helix. Alternating deoxyribose andphosphate groups on thebackbone form the outsideof the helix.

The planar purine andpyrimidine bases of bothstrands are stacked insidethe helix.

DNA str ct re


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DNA structure

10/10/05 35

Fig. 8-15

The furanose ring usually ispuckered in a C-2' endoconformation in DNA.

The offset of therelationship of the base pairsto the strands gives a majorand a minor groove.

In B-form DNA (mostcommon) the depths of themajor and minor grooves aresimilar to each other.

Base stacking in DNA


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Base stacking in DNA

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Berg Fig. 1.4; 5.13

C-G (red) and A-T (blue) basepairs are isosteric (same shapeand size), allowing stacking alonga helical axis for any sequence.

Base pairs stackinside the helix.

DNA strands


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DNA strands

10/10/05 37

Fig. 8-16

The antiparallel strands of DNA arenot identical, but are complementary.

This means that they are positionedto align complementary base pairs: Cwith G, and A with T.

So you can predict the sequence ofone strand given the sequence of itscomplement.

Useful for information storageand transfer!

Note sequence conventionally is givenfrom the 5' to 3' end

Nucleic acids


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Nucleic acids

10/10/05 38 Fig. 8-19

B form - The most commonconformation for DNA.

A form - common for RNAbecause of different sugarpucker. Deeper minor groove,shallow major groove

A form is favored in conditionsof low water. Z form - narrow, deep minor

groove. Major groove hardlyexistent. Can form for some

DNA sequences; requiresalternating syn and anti baseconfigurations.

36 base pairs

Backbone - blue;Bases- gray

Nucleic acids


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Nucleic acids

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Fig. 8-19

RNA has a rich and varied structure


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RNA has a rich and varied structure

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Fig. 8-26

Watson-

Crick base pairs(helical segments;Usually A-form).Helix is secondarystructure.Note A-U pairs inRNA.

DNA canformstructureslike this aswell.

RNA displays interesting tertiary structure


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RNA displays interesting tertiary structure

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Fig. 8-28Fig. 8-25

Single-strandedRNAright-handedhelix

T. thermophila intron,A ribozyme (RNA enzym (1GRZ)

Hammerhead ribozyme(1MME)

Yeast tRNAPhe(1TRA)

The mother of all biomolecules


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The mother of all biomolecules

42

1ffk

Large subunit of the ribosome (proteins at least)

4. nukleotida, dna,rna ok

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