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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
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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
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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
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Fig. 6-30
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Structure of nucleotides
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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
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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
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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
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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
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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
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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
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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
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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
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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
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1ffk
Large subunit of the ribosome (proteins at least)