Chapter 2 Structure and function of nucleic acid

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Chapter 2 Structure and function of nucleic
acid
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Contents

• Composition of nucleic acids
• Structure and function of DNA
• Structures and functions of RNA
• Properties of nucleic acid

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Deoxyribonucleic acid, DNA
Nucleic acid
Ribonucleic acid, RNA
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Section 1 Composition of nucleic acids
Nucleic acids(??)
Nucleotides(???)
Nucleosides (??)
phosphate(??)
Bases (??) purines ?? pyrimidines ??
ribose(??) ribose ?? deoxyribose D-2-????
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1. Bases ??

• Purines and pyrimidines
• Purines (??)
• adenine (???), guanine (???)
• Pyrimidines (??)

cytosine (???), thymine (????)
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• 2. Ribose (in RNA) and deoxyribose (in DNA)
• ???????

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• 3. Ribonucleosides??
• Ribonucleoside ribose/deoxyribose
• bases

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The common ribonucleosides-cytidine, uridine,
adenosine and guanosine. Also inosine drawn in
anti conformation.
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• 4. Nucleotides ???
• Nucleotide nucleoside phosphate

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5. Nucleoside diphosphates and triphosphates
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• 6. Polynucleic acid chain ?????

Polynucleic acid chain connected nucleotides
binding by 35phosphodiester bonds (35?????)
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3,5phosphodiester bridges link nucleotides
together to form polynucleotide chains
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• 7. Some important nucleotides
• dATP, dGTP, dCTP, dUTPraw materials for DNA
  biosynthesis DNA?????.
• ATP, GTP, CTP, GTP
• raw materials for RNA biosynthesis RNA?????
• energy donor ?????
• Important co-enzymes ????
• Cycling nucleotidescAMP, cGMP secondary
  messengers in hormones action. ???????????

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cAMP ???? and cGMP????
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• Section 2 Structure and function of DNA

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• Primary structure
• The base sequence(????) in polydeoxynucleotide
  chain.
• The smallest DNA in nature is virus(??) DNA. The
  length of fX174 virus DNA is 5,386 bases (a
  single chain). The DNA length of human genome is
  3,000,000,000 pair bases.

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• 2. Secondary structure
• DNA double helix structure

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Francis H.C. Crick
James D. Watson
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• Key points on DNA double helic structure
• DNA is composed of two strand wound round each
  other to form a double helix. The two DNA stands
  are organized in an antiparallel arrangement the
  two strands run in opposite directions, one
  strand is oriented 5?3 and the other is
  oriented 3 ?5.
• The bases on the inside and the sugar-phosphate
  backbones (??)on the outside.
• The diameter of the double helix is 2 nm, the
  distance between two base is 0.34 nm, each turn
  of the helix involves 10 bases pairs, 34 nm.

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• (4) The bases of two strands form hydrogen
  bonds to each other, A pairs with T, G pairs with
  C. this is called complementary base
  pairing??????.
• (5) stable configuration???? can be maintained by
  hydrogen bond and base stacking force?????

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The antiparallel nature of the DNA double helix
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• Conformational variation in double-helical
  structure
• B-DNA
• A-DNA
• Z-DNA

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• 3. Tertiary structure Supercoils
• Supercoils double-stranded circular DNA
  form supercoils if the strands are underwound
  (negatively supercoiled) or overwound (positively
  supercoiled).

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The DNA interwinds and wraps about itsself
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Supercoils in long, linear DNA arranged into
loops whose ends are restrained-model for
chromosomal DNA
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• The DNA in a prokaryotic cell is a supercoil.
• The DNA in eukaryotic cell is packaged into
  chromosomes.

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Eukaryotic chromosomes(?????)

• Nucleosome(???)
• ?
• 30nm fiber(??)
• ?
• Radial loops(??)
• ?
• Rosette(????)
• ?
• Coid(???)
• ?
• Chromatid(????)
• ?
• Chromosome(???)

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Nucleosome

• Histones interact ionically with
• the anionic phosphate groups in
• the DNA backbone to form
• nucleosomes, structures in
• which the DNA double helix is
• wound around a protein core
• composed of pairs of four
• different histone polypeptides.

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Functions of DNA

• The carrier of genetic information.
• The template strand involved in replication and
  transcription.

• Gene(??) the minimum functional unit in DNA

• Genome(???) the total genes in a living cell or
  living beings.

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Section 3 Structures and functions of RNA

• Types
• mRNA messenger RNA, the carrier of genetic
  information from DNA to translate into protein
• tRNA transfer RNA , to transport amino acid to
  ribosomes to synthesize protein
• rRNA ribosome RNA, the components of ribosomes
• hnRNA Heterogeneous nuclear RNA (?????RNA)
• snRNA small nuclear RNA (???RNA)
• Ribozyme(??)

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RNA structure

• RNA molecules are largely single-stranded but
  there are double-stranded regions.

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Massager RNA( mRNA)

• The carrier of genetic information from DNA for
  the synthesis of protein. Composition vary
  considerably in size (500-6000bases in E. coli)

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Eukaryotic mRNA Structure

• Capping linkage of 7-methylguanosine 7-?????to
  the 5 terminal residue.
• (2) Tailing attachment of an adennylate polymer
  (poly A ??A)

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• ????mRNA???

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Ribosome RNA (rRNA)

• A component of ribosomes.
• Ribosomes are cytoplasmic structures that
  synthesize protein, composed of both proteins
  and rRNA.
• The ribosomes of prokaryotes and eukaryotes are
  similar in shape and function. The difference
  between them is the size and chemical composition.

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The organization and composition of prokaryotic
and eukaryotic ribosomes
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The proposed secondary structure for E. coli
16S rRNA
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Transfer RNA (tRNA)
Function Transport amino acids to ribosomes for
assembly into proteins.

• Primary Structure
• Average length 75 bases
• Modified bases pseudouridine
• methylguanosine
  
• dihydrouridine
• The sequence CCA at the 3 terminus

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Secondary structure warped cloverleaf ???

• Four loops and four arms????
• Amino acid arm????(7bp) to bide amino acid
• D loop(8-14bp) D-?and D arm(3-4bp)
• Anticode loop(5bp) ????and arm(7bp) to recognize
  amino acid
• T?C loop(7bp) T?C ?and arm(5bp)
• Variable loop(4-5bpor 13-21bp)???

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A general diagram for the structure of tRNA
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The complete nucleotid sequence and cloverleaf
structure of yeast Alanine tRNA
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(a)the three-dimensional structure of yeast
phenylalanine Trna as deduced from X-ray
diffraction studies of its crystal. (b)a
space-filling model of the molecule.
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Section 4 Properties of nucleic acid

• General physical and chemical properties
• Amphiphilic ?? molecules normally acidic because
  of phosphate.
• Solid DNA white fiber RNA white powder.
  Insoluble in organic solvents, can be precipitate
  by ethanol.
• Can be hydrolyzed by acid/alkaline/enzymes

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2. UV Absorption ????

• Specific absorption at 260nm.
• This can be used to identify nucleic acid

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The UV absorption spectra of the common
ribonucleotides
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3. Denaturation ??

• Concept
• the course of hydrogen bonds broken, 3-D
  structure was destroyed, the double helix changed
  into single strand irregular coid
• Results
• the value of 260nm absorption is increased
• Viscous ?? is decreased
• biological functions are lost

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• Heat denaturation and Tm

When DNA were heated to certain temperature,
the absorption value at 260nm would increased
sharply,which indicates that the double strand
helix DNA was separated into single strand. When
the absorption value increases to 40, the value
change would low down, which indicates the double
strands had been completely separated.
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DNA denaturation and Tm
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• Tm melting temperature of DNA
• The temperature of UV absorption increase to
  an half of maximum value in DNA denaturation.
• Factors affect Tm
• G-C content there are three hydrogen
  bonds between G-C pair. The more G-C content, the
  higher Tm value.
• (GC) (Tm-69.3) 2.44

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Tm of two DNA molecules with different GC
content
Less GC
Higher GC
Temperature
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4. Renaturation of DNA

• When slowly cooling down the denatured DNA
  solution, the single strand DNA can reform a
  double strands helix to recover its biological
  functions.

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5. Molecule hybridization ????

• During the course of lowing down denaturing
  temperature, between different resource DNAs or
  single stand DNA and mRNA with complementary
  bases will repair into a double strands to form
  a hybrid DNA or DNA-RNA . This course is called
  molecule hybridization.

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