24 24-1 © 2003 Thomson Learning, Inc. All rights reserved General, Organic, and Biochemistry, 7e...

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24-1© 2003 Thomson Learning, Inc.All rights reserved

General, Organic, and General, Organic, and Biochemistry, 7eBiochemistry, 7e

Bettelheim,Bettelheim,

Brown, and MarchBrown, and March

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Chapter 24Chapter 24

Nucleotides, Nucleic Nucleotides, Nucleic Acids, and HeredityAcids, and Heredity

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IntroductionIntroduction• each cell of our bodies contains thousands of different

proteins• how do cells know which proteins to synthesize out of

the extremely large number of possible amino acid sequences?

• from the end of the 19th century, biologists suspected that the transmission of hereditary information took place in the nucleus, more specifically in structures called chromosomeschromosomes

• the hereditary information was thought to reside in genesgenes within the chromosomes

• chemical analysis of nuclei showed chromosomes are made up largely of proteins called histoneshistones and nucleic nucleic acidsacids

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IntroductionIntroduction• by the 1940s it became clear that deoxyribonucleic deoxyribonucleic

acids (DNA)acids (DNA) carry the hereditary information• other work in the 1940s demonstrated that each gene

controls the manufacture of one protein• thus, the expression of a gene in terms of an enzyme

protein led to the study of protein synthesis and its control

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Nucleic AcidsNucleic Acids• There are two kinds of nucleic acids in cells

• ribonucleic acids (RNA)• deoxyribonucleic acids (DNA)

• Both RNA and DNA are polymers built from monomers called nucleotides

• A nucleotide is composed of • a base• a monosaccharide• a phosphate

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Pyrimidine/Purine BasesPyrimidine/Purine BasesHN

NO

H

N

N

NH2

H

HN

N

H

CH3

Uracil (U)(in RNA)

Thymine (T)(DNA andsome RNA)

Cytosine (C)(DNA andsome RNA)

N

N

Pyrimidine

1

2

3

4

5

6

HN

N N

NO

HH2N

Guanine (G)(DNA and RNA)

N

N N

N

NH2

HAdenine (A)

(DNA and RNA)

N

N N

N

HPurine

1

2

3

4

56 7

8

9

O O

O O

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NucleosidesNucleosides• Nucleoside:Nucleoside: a compound that consists of D-

ribose or 2-deoxy-D-ribose bonded to a purine or pyrimidine base by a -N-glycosidic bond

HH

HH

OHOCH2

HO OH

O

O

HN

N

anomericcarbon

a -N-glycosidicbond

Uridine

-D-riboside

uracil

1'

2'3'

4'

5'1

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NucleotidesNucleotides• NucleotideNucleotide:: a nucleoside in which a molecule of

phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’ or the 5’-OH

O-

-O-P-O-CH2

OO

H

H

OH

H

HOH

N

N N

N

NH2

5'

1'

3'

Adenosine 5'-monophosphate(5'-AMP)

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NucleotidesNucleotides• deoxythymidine 3’-monophosphate (3’-dTMP)

O

H

H

H

H

OH

HN

N

OCH3

O

P

O-

O O-

HOCH2

5'

1'

3'

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NucleotidesNucleotides• adenosine 5’-triphosphate (ATP) serves as a common

currency into which energy gained from food is converted and stored

HH

H

O

HO OH

N

N

N

N

NH2

-O-P-O-P-O-P-O-CH2

O

O-O-

O

O-

H

O

Adenosine 5'-triphosphate(ATP)

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Structure of DNA and RNAStructure of DNA and RNA• Primary Structure:Primary Structure: the sequence of bases along

the pentose-phosphodiester backbone of a DNA or RNA molecule• base sequence is read from the 5’ end to the 3’ end

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Nucleic Acid - 1° Nucleic Acid - 1° StructureStructure

• A schematic diagram of a nucleic acid

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DNA - 2° StructureDNA - 2° Structure• Secondary structureSecondary structure:: the ordered arrangement of

nucleic acid strands• the double helix model of DNA 2° structure was

proposed by James Watson and Francis Crick in 1953

• Double helixDouble helix:: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis

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The DNA The DNA Double Double HelixHelix

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Base PairingBase Pairing

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Higher Structure of DNAHigher Structure of DNA• DNA is coiled around proteins called histoneshistones• histones are rich in the basic amine acids Lys and Arg,

whose side chains have a positive charge• the negatively-charged DNA molecules and positively-

charged histones attract each other and form units called nucleosomes

• nucleosome:nucleosome: a core of eight histone molecules around which the DNA helix is wrapped

• nucleosomes are further condensed into chromatinchromatin• chromatin fibers are organized into loops, and the

loops into the bands that provide the superstructure of chromosomeschromosomes

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ChromosomesChromosomes

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DNA and RNADNA and RNA• The three differences in structure between DNA

and RNA are• DNA bases are A, G, C, and TT; the RNA bases are A, G,

C, and UU• the sugar in DNA is 2-deoxy-D-ribose2-deoxy-D-ribose; in RNA it is D-D-

riboseribose• DNA is always double strandeddouble stranded; there are several kinds

of RNA, all of which are single-strandedsingle-stranded

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RNARNA• RNA molecules are classified according to their

structure and function

RNA type Size Function

Transfer(tRNA)

Ribosomal(rRNA)

Messenger(mRNA)

from 73 to 93 base pairs

very large;MW up to 106

combines with proteinsto form ribosomes

750 base pairson average

transports amino acidsto the site of proteinsynthesis

directs amino acidsequence of proteins

Ribozymes(catalytic RNA)

catalyze cleavage of partof their own sequencesin mRNA and tRNA

very large

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Structure of tRNAStructure of tRNA

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Genes, Exons, and IntronsGenes, Exons, and Introns• Gene:Gene: a segment of DNA that carries a base

sequence that directs the synthesis of a particular protein, tRNA, or mRNA• there are many genes in one DNA molecule• in bacteria the gene is continuous• in higher organisms the gene is discontinuous

• Exon:Exon: a section of DNA that, when transcribed, codes for a protein or RNA

• Intron:Intron: a section of DNA that does not code for anything functional

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Genes, Exons, and IntronsGenes, Exons, and Introns• introns are cut out of mRNA before the protein is

synthesized

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DNA ReplicationDNA Replication• ReplicationReplication involves separation of the two

original strands and synthesis of two new daughter strands using the original strands as templates• DNA double helix unwinds at a specific point called an

origin of replicationorigin of replication• polynucleotide chains are synthesized in both

directions from the origin of replication; that is, DNA replication is bidirectionalbidirectional

• at each origin of replication, there are two replication replication forksforks, points at which new polynucleotide strands are formed

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DNA ReplicationDNA Replication• DNA is synthesized from its 5’ -> 3’ end (from the 3’ ->

5’ direction of the template)• the leading strand leading strand is synthesized continuously in the 5’

-> 3’ direction toward the replication fork • the lagging strand lagging strand is synthesized semidiscontinuously

as a series of Okazaki fragmentsOkazaki fragments, also in the 5’ -> 3’ direction, but away from the replication fork

• Okazaki fragments of the lagging strand are joined by the enzyme DNA ligaseDNA ligase

• replication is semiconservativesemiconservative:: each daughter strand contains one template strand and one newly synthesized strand

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DNA ReplicationDNA Replication

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ReplisomesReplisomes• Replisomes are assemblies of “enzyme factories”

Component Function

HelicasesPrimaseClamp proteinDNA polymeraseLigase

Unwinds the DNA double helixSynthesizes primersThreads leading strandJoins assembled nucleotidesJoins Okazaki fragments

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DNA ReplicationDNA Replication• Opening up the superstructure

• during replication, the very condensed superstructure of chromosomes is opened by a signal transduction mechanism

• one step of this mechanism involves acetylation and deacetylation of key lysine residues

• acetylation removes a positive charge and thus weakens the DNA-histone interactions

Lys-CH2CH2CH2CH2NH3+

Lys-CH2CH2CH2CH2NH-CCH3

OLysine side chain

(has a positive charge)

Acetylated lysine side chain(has no charge)

acetylation

deacetylation

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DNA ReplicationDNA Replication• Relaxation of higher structures of DNA

• tropoisomerases tropoisomerases (also called(also called gyrases gyrases)) facilitate the relaxation of supercoiled DNA by introducing either single strand or double strand breaks in the DNA

• once the supercoiling is relaxed by this break, the broken ends are joined and the tropoisomerase diffuses from the location of the replication fork

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DNA ReplicationDNA Replication• Unwinding the DNA double helix

• replication of DNA starts with unwinding of the double helix

• unwinding can occur at either end or in the middle• unwinding proteins called helicaseshelicases attach themselves

to one DNA strand and cause separation of the double helix

• the helicases catalyze the hydrolysis of ATP as the DNA strand moves through; the energy of hydrolysis promotes the movement

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DNA ReplicationDNA Replication• Primer/primases

• primersprimers are short oligonucleotides of four to 15 nucleotides long

• they are required to start the synthesis of both daughter strands

• primasesprimases are enzymes that catalyze the synthesis of primers

• primases are placed at about every 50 nucleotides in the lagging strand synthesis

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DNA ReplicationDNA Replication• DNA polymerasesDNA polymerases are key enzymes in replication

• once the two strands have separated at the replication fork, the nucleotides must be lined up in proper order for DNA synthesis

• in the absence of DNA polymerase, alignment is slow• DNA polymerase provides the speed and specificity of

alignment• along the lagging (3’ -> 5’) strand, the polymerases can

synthesize only short fragments, because these enzymes only work from 5’ -> 3’

• these short fragments are called Okazaki fragmentsOkazaki fragments• joining the Okazaki fragments and any remaining nicks

is catalyzed by DNA ligaseDNA ligase

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DNA RepairDNA Repair• The viability of cells depends on DNA repair

enzymes that can detect, recognize, and repair mutations in DNA

• Base excision repairBase excision repair (BER)(BER): one of the most common repair mechanisms• a specific DNA glycosylase recognizes the damaged

base• it catalyzes the hydrolysis of the -NN-glycosidic bond

between the incorrect base and its deoxyribose• it then flips the damaged base, completing the excision• the sugar-phosphate backbone remains intact

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DNA RepairDNA Repair• BER (cont’d)

• at the APAP (apapurinic or apapyrimidinic) sitesite thus created, an endonucleasendonuclease catalyzes the hydrolysis of the backbone

• an exonucleaseexonuclease liberates the sugar-phosphate unit of the damaged site

• DNA polymerase inserts the correct nucleotide• DNA ligase seals the backbone to complete the repair

• NERNER (nnucleotide eexcision rrepair) removes and repairs up to 24-32 units by a similar mechanism involving a number of repair enzymes

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CloningCloning• Clone:Clone: a genetically identical population• Cloning:Cloning: a process whereby DNA is amplified by

inserting it into a host and having the host replicate it along with the host’s own DNA

• Polymerase chain reaction (PCR):Polymerase chain reaction (PCR): an automated technique for amplifying DNA using a heat-stable DNA polymerase from a thermophilic bacterium

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CloningCloning

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End End Chapter 24Chapter 24

Nucleic AcidsNucleic Acids

24 24-1 © 2003 Thomson Learning, Inc. All rights reserved General, Organic, and Biochemistry, 7e...

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