Dna,rna

Dr. Wolf's CHM 424 28- 1
Nucleic AcidsNucleic Acids

28.128.1
Pyrimidines and PurinesPyrimidines and Purines

Pyrimidines and PurinesPyrimidines and PurinesPyrimidines and PurinesPyrimidines and Purines
In order to understand the structure andIn order to understand the structure and
properties of DNA and RNA, we need to look atproperties of DNA and RNA, we need to look at
their structural components.their structural components.
We begin with certain heterocyclic aromaticWe begin with certain heterocyclic aromatic
compounds called pyrimidines and purines.compounds called pyrimidines and purines.

Pyrimidine and purine are the names of thePyrimidine and purine are the names of the
parent compounds of two types of nitrogen-parent compounds of two types of nitrogen-
containing heterocyclic aromatic compounds.containing heterocyclic aromatic compounds.
PyrimidinePyrimidine PurinePurine
NN
NN NN
HH
NN
NNNN 11
22
33
44
5577
88
99
11
22
33
44
55
66
66

Amino-substituted derivatives of pyrimidine andAmino-substituted derivatives of pyrimidine and
purine have the structures expected from theirpurine have the structures expected from their
names.names.
4-Aminopyrimidine4-Aminopyrimidine 6-Aminopurine6-Aminopurine
HH
NN NN
NNNN
HH
HH
NNHH22
NN
NN
HH
HH
HHHH22NN

But hydroxy-substituted pyrimidines and purinesBut hydroxy-substituted pyrimidines and purines
exist in keto, rather than enol, forms.exist in keto, rather than enol, forms.
enolenol
NN
NN
HH
HH
HHHHOO
NN
NN
HH
HH
HHOO
HH
ketoketo

But hydroxy-substituted pyrimidines and purinesBut hydroxy-substituted pyrimidines and purines
exist in keto, rather than enol, forms.exist in keto, rather than enol, forms.
HH
NN NN
NNNN
HH
HH
OOHH
enolenol ketoketo
HH
NN NN
NN
HH
HH
OO
HHNN

Important PyrimidinesImportant PyrimidinesImportant PyrimidinesImportant Pyrimidines
Pyrimidines that occur in DNA are cytosine andPyrimidines that occur in DNA are cytosine and
thymine. Cytosine and uracil are thethymine. Cytosine and uracil are the
pyrimidines in RNA.pyrimidines in RNA.
HHNN
NN
HH
OO
OO
UracilUracil
HHNN
NN
HH
OO
OO
CHCH33
ThymineThymine
HHNN
NN
HH
NNHH22
OO
CytosineCytosine

Important PurinesImportant PurinesImportant PurinesImportant Purines
Adenine and guanine are the principal purinesAdenine and guanine are the principal purines
of both DNA and RNA.of both DNA and RNA.
AdenineAdenine
NN
NN
NNHH22
NN
NN
HH
GuanineGuanine
OO
HHNN
NN
HH
NN
NN
HH22NN

Caffeine and TheobromineCaffeine and TheobromineCaffeine and TheobromineCaffeine and Theobromine
Caffeine (coffee) and theobromine (coffee andCaffeine (coffee) and theobromine (coffee and
tea) are naturally occurring purines.tea) are naturally occurring purines.
CaffeineCaffeine
NN
NN
OO
NN
NN
HH33CC
OO
CHCH33
CHCH33
TheobromineTheobromine
OO
HHNN
NNNN
NN
CHCH33
CHCH33
OO

28.228.2
NucleosidesNucleosides

NucleosidesNucleosidesNucleosidesNucleosides
The classical structural definition is that aThe classical structural definition is that a
nucleoside is a pyrimidine or purine N-glycosidenucleoside is a pyrimidine or purine N-glycoside
ofof DD-ribofuranose or 2-deoxy--ribofuranose or 2-deoxy-DD-ribofuranose.-ribofuranose.
Informal use has extended this definition toInformal use has extended this definition to
apply to purine or pyrimidine N-glycosides ofapply to purine or pyrimidine N-glycosides of
almost any carbohydrate.almost any carbohydrate.
The purine or pyrimidine part of a nucleoside isThe purine or pyrimidine part of a nucleoside is
referred to as areferred to as a purine or pyrimidine basepurine or pyrimidine base..

NNHH22
HOHO OHOH
OOHOCHHOCH22
OO
NN
NN
Table 28.2Table 28.2Table 28.2Table 28.2
Pyrimidine nucleosidesPyrimidine nucleosides
Cytidine occurs in RNA;Cytidine occurs in RNA;
its 2-deoxy analog occurs in DNAits 2-deoxy analog occurs in DNA
CytidineCytidine

OO
NN
NNHH
OO
HOHO
OO
HH33CC
HOCHHOCH22
Thymidine occurs in DNAThymidine occurs in DNA
ThymidineThymidine

HOCHHOCH22
OO
NN
NNHH
OO
OHOHHOHO
OO
Uridine occurs in RNAUridine occurs in RNA
UridineUridine

Purine nucleosidesPurine nucleosides
AdenosineAdenosine
Adenosine occurs in RNA;Adenosine occurs in RNA;
HOCHHOCH22 OO
OHOHHOHO
NN
NN
NN
NHNH22
NN

Purine nucleosidesPurine nucleosides
GuanosineGuanosine
Guanosine occurs in RNA;Guanosine occurs in RNA;
HOCHHOCH22
NN
NHNH
OO
OO
HOHO
NN NHNH22
NN
OHOH

28.328.3
NucleotidesNucleotides
Nucleotides are phosphoric acid esters ofNucleotides are phosphoric acid esters of
nucleosides.nucleosides.

Adenosine 5'-Monophosphate (AMP)Adenosine 5'-Monophosphate (AMP)Adenosine 5'-Monophosphate (AMP)Adenosine 5'-Monophosphate (AMP)
Adenosine 5'-monophosphate (AMP) is alsoAdenosine 5'-monophosphate (AMP) is also
called 5'-adenylic acid.called 5'-adenylic acid.
OCHOCH22PPHOHO
OO
HOHO
OO
OHOHHOHO
NN
NN
NN
NHNH22
NN
5'5'
1'1'
2'2'3'3'
4'4'

Adenosine Diphosphate (ADP)Adenosine Diphosphate (ADP)Adenosine Diphosphate (ADP)Adenosine Diphosphate (ADP)
OOPP
OO
HOHO
HOHO OCHOCH22PP
OO
HOHO
OO
OHOHHOHO
NN
NN
NN
NHNH22
NN

Adenosine Triphosphate (ATP)Adenosine Triphosphate (ATP)Adenosine Triphosphate (ATP)Adenosine Triphosphate (ATP)
OOPP
OO
HOHO
OO OCHOCH22PP
OO
HOHO
OO
OHOHHOHO
NN
NN
NN
NHNH22
NN
PP
OO
HOHO
HOHO
ATP is an important molecule in severalATP is an important molecule in several
biochemical processes including:biochemical processes including:
energy storage (Sections 28.4-28.5)energy storage (Sections 28.4-28.5)
phosphorylationphosphorylation

cAMP and cGMPcAMP and cGMPcAMP and cGMPcAMP and cGMP
Cyclic AMP and cyclic GMP areCyclic AMP and cyclic GMP are
"second messengers" in many"second messengers" in many
biological processes. Hormonesbiological processes. Hormones
(the "first messengers")(the "first messengers")
stimulate the formation of cAMPstimulate the formation of cAMP
and cGMP.and cGMP.
Cyclic adenosine monophosphate (cAMP)Cyclic adenosine monophosphate (cAMP)
CHCH22 OO
OHOH
NN
NN
NN
NHNH22
NN
OO
OO
PP
OO
HOHO

cAMP and cGMPcAMP and cGMPcAMP and cGMPcAMP and cGMP
Cyclic AMP and cyclic GMP areCyclic AMP and cyclic GMP are
"second messengers" in many"second messengers" in many
biological processes. Hormonesbiological processes. Hormones
(the "first messengers")(the "first messengers")
stimulate the formation of cAMPstimulate the formation of cAMP
and cGMP.and cGMP.
OO
OO
PP
OO
HOHO
Cyclic guanosine monophosphate (cGMP)Cyclic guanosine monophosphate (cGMP)
CHCH22
NN
NHNH
OO
OO
NN NHNH22
NN
OHOH

28.628.6
Phosphodiesters,Phosphodiesters,
Oligonucleotides, andOligonucleotides, and
PolynucleotidesPolynucleotides

PhosphodiestersPhosphodiestersPhosphodiestersPhosphodiesters
A phosphodiester linkage between twoA phosphodiester linkage between two
nucleotides is analogous to a peptide bondnucleotides is analogous to a peptide bond
between two amino acids.between two amino acids.
Two nucleotides joined by a phosphodiesterTwo nucleotides joined by a phosphodiester
linkage gives a dinucleotide.linkage gives a dinucleotide.
Three nucleotides joined by twoThree nucleotides joined by two
phosphodiester linkages gives a trinucleotide,phosphodiester linkages gives a trinucleotide,
etc. (See next slide)etc. (See next slide)
A polynucleotide of about 50 or fewerA polynucleotide of about 50 or fewer
nucleotides is called annucleotides is called an oligonucleotide.oligonucleotide.

3'
5'
HOCH2
O
O
N
N
N
N
P OCH2O
HO
NH2
OCH2
O
NH
N
N
N
HO
O
NH2
HO
O P
H3C
O
O
O
O
NH
N
Fig. 28.1Fig. 28.1
TheThe
trinucleotidetrinucleotide
ATGATG
Fig. 28.1Fig. 28.1
TheThe
trinucleotidetrinucleotide
ATGATG
phosphodiesterphosphodiester
linkageslinkages
between 3' ofbetween 3' of
one nucleotideone nucleotide
and 5' of theand 5' of the
nextnext
AA
TT
GG
free 5' endfree 5' end
free 3' endfree 3' end

28.728.7
Nucleic AcidsNucleic Acids
Nucleic acids are polynucleotides.Nucleic acids are polynucleotides.

Nucleic AcidsNucleic AcidsNucleic AcidsNucleic Acids
Nucleic acids first isolated in 1869 (JohannNucleic acids first isolated in 1869 (Johann
Miescher)Miescher)
Oswald Avery discovered (1945) that aOswald Avery discovered (1945) that a
substance which caused a change in thesubstance which caused a change in the
genetically transmitted characteristics of agenetically transmitted characteristics of a
bacterium was DNA.bacterium was DNA.
Scientists revised their opinion of the function ofScientists revised their opinion of the function of
DNA and began to suspect it was the majorDNA and began to suspect it was the major
functional component of genes.functional component of genes.

Composition of DNAComposition of DNAComposition of DNAComposition of DNA
Erwin Chargaff (Columbia Univ.) studied DNAsErwin Chargaff (Columbia Univ.) studied DNAs
from various sources and analyzed thefrom various sources and analyzed the
distribution of purines and pyrimidines in them.distribution of purines and pyrimidines in them.
The distribution of the bases adenine (A),The distribution of the bases adenine (A),
guanine (G), thymine (T), and cytosine (C)guanine (G), thymine (T), and cytosine (C)
varied among species.varied among species.
But the total purines (A and G) and the totalBut the total purines (A and G) and the total
pyrimidines (T and C) were always equal.pyrimidines (T and C) were always equal.
Moreover: %A = %T, and %G = %CMoreover: %A = %T, and %G = %C

Composition of Human DNAComposition of Human DNAComposition of Human DNAComposition of Human DNA
Adenine (A) 30.3%Adenine (A) 30.3% Thymine (T) 30.3%Thymine (T) 30.3%
Guanine (G) 19.5%Guanine (G) 19.5% Cytosine (C) 19.9%Cytosine (C) 19.9%
Total purines: 49.8%Total purines: 49.8% Total pyrimidines: 50.1%Total pyrimidines: 50.1%
For example:For example:
PurinePurine PyrimidinePyrimidine

Structure of DNAStructure of DNAStructure of DNAStructure of DNA
James D. Watson and Francis H. C. CrickJames D. Watson and Francis H. C. Crick
proposed a structure for DNA in 1953.proposed a structure for DNA in 1953.
Watson and Crick's structure was based on:Watson and Crick's structure was based on:
•Chargaff's observations•Chargaff's observations
•X-ray crystallographic data of Maurice•X-ray crystallographic data of Maurice
Wilkins and Rosalind FranklinWilkins and Rosalind Franklin
•Model building•Model building

28.828.8
Secondary Structure of DNA:Secondary Structure of DNA:
The Double HelixThe Double Helix

FORMS OF DNAFORMS OF DNAFORMS OF DNAFORMS OF DNA

Base PairingBase PairingBase PairingBase Pairing
Watson and Crick proposed that A and T wereWatson and Crick proposed that A and T were
present in equal amounts in DNA because ofpresent in equal amounts in DNA because of
complementary hydrogen bonding.complementary hydrogen bonding.
2-deoxyribose2-deoxyribose N
NN
N N
H
H
N
N
O CH3
O
H
2-deoxyribose2-deoxyribose
AA TT

Watson and Crick proposed that A and T wereWatson and Crick proposed that A and T were
present in equal amounts in DNA because ofpresent in equal amounts in DNA because of
complementary hydrogen bonding.complementary hydrogen bonding.

Likewise, the amounts of G and C in DNA wereLikewise, the amounts of G and C in DNA were
equal because of complementary hydrogenequal because of complementary hydrogen
bonding.bonding.
N
NN
N O
N
H
H
H
N
N
N
O
H
H
GG CC

Likewise, the amounts of G and C in DNA wereLikewise, the amounts of G and C in DNA were
equal because of complementary hydrogenequal because of complementary hydrogen
bonding.bonding.

The DNA DuplexThe DNA DuplexThe DNA DuplexThe DNA Duplex
Watson and Crick proposed a double-strandedWatson and Crick proposed a double-stranded
structure for DNA in which a purine orstructure for DNA in which a purine or
pyrimidine base in one chain is hydrogenpyrimidine base in one chain is hydrogen
bonded to its complement in the other.bonded to its complement in the other.
••Gives proper Chargaff ratios (A=T and G=C)Gives proper Chargaff ratios (A=T and G=C)
••Because each pair contains one purine andBecause each pair contains one purine and
one pyrimidine, the A---T and G---C distancesone pyrimidine, the A---T and G---C distances
between strands are approximately equal.between strands are approximately equal.
••Complementarity between strands suggests aComplementarity between strands suggests a
mechanism for copying genetic information.mechanism for copying genetic information.

O
O
Ğ
O
Ğ
O
Ğ
O
O
O
O
O
OP
O
O
P O
O
O
P O
O
O
O
O
O
Ğ
O
Ğ
O
Ğ
O
O
O
O
O P
O
O
PO
O
O
PO
O
O
C G
AT
AT
CG
3'
5'
5'
5'
5' 5'
5'
5'
5'
3'
3'
3'
3'
3'
3'
3'
Fig. 28.4Fig. 28.4Fig. 28.4Fig. 28.4
Two antiparallelTwo antiparallel
strands of DNAstrands of DNA
are paired byare paired by
hydrogen bondshydrogen bonds
between purinebetween purine
and pyrimidineand pyrimidine
bases.bases.

Fig. 28.5Fig. 28.5Fig. 28.5Fig. 28.5
Helical structure ofHelical structure of
DNA. The purineDNA. The purine
and pyrimidineand pyrimidine
bases are on thebases are on the
inside, sugars andinside, sugars and
phosphates on thephosphates on the
outside.outside.

28.928.9
Tertiary Structure of DNA:Tertiary Structure of DNA:
SupercoilsSupercoils

DNA is coiledDNA is coiledDNA is coiledDNA is coiled
A strand of DNA is too long (about 3 cm inA strand of DNA is too long (about 3 cm in
length) to fit inside a cell unless it is coiled.length) to fit inside a cell unless it is coiled.
Random coiling would reduce accessibility toRandom coiling would reduce accessibility to
critical regions.critical regions.
Efficient coiling of DNA is accomplished with theEfficient coiling of DNA is accomplished with the
aid of proteins calledaid of proteins called histones.histones.

HistonesHistonesHistonesHistones
Histones are proteins rich in basic amino acidsHistones are proteins rich in basic amino acids
such as lysine and arginine.such as lysine and arginine.
Histones are positively charged at biological pH.Histones are positively charged at biological pH.
DNA is negatively charged.DNA is negatively charged.
DNA winds around histone proteins to formDNA winds around histone proteins to form
nucleosomes.nucleosomes.

Each nucleosome contains one and three-quartersEach nucleosome contains one and three-quarters
turns of coil = 146 base pairs.turns of coil = 146 base pairs.
Linker contains about 50 base pairs.Linker contains about 50 base pairs.

NucleosomeNucleosome == Histone proteinsHistone proteins + Supercoiled DNA+ Supercoiled DNA

28.1028.10
Replication of DNAReplication of DNA

Fig. 28.8 DNA ReplicationFig. 28.8 DNA Replication
A T C C G T A G G A T T A GC
5'3'
AT G CG A T C C T G A A T C
3'5'
The DNA to be copied is a double helix, shown here as
flat for clarity.
The two strands begin to unwind. (next slide)

A T C C G T A G
G
A
T
T A
G
C
AT G CG A
T
C
C T
G
A
A
T C
3'
5'
5'
3'
Each strand will become a template for construction of
its complement.

A'
T'
G'
C'
A T C C G T
A G
G A
T
T A G
C
5'
3'
AT G CG A
T
C
C T
G
A
A
T C
5'
5'
T' A'
3'
3'
leading strand
lagging strand
3'
5'
C'T'
A'A'
Two new strands form as nucleotides that are
complementary to those of the original strands are
joined by phosphodiester linkages.
Polynucleotide chains grow in
the 5'-3' direction—continuous in
the leading strand, discontinuous
in the lagging strand.

A' T' C' C' G' T' A' G' G' A' T' T' A' G'C'
5'3'
AT G CG A T C C T G A A T C
3'5'
A T C C G T A G G A T T A GC
5'3'
A'T' G' C'G' A' T' C' C' T' G' A' A' T' C'
3'5'
+
Two duplex DNAs result, each of which is identical to
the original DNA.

Elongation of the growing DNA chainElongation of the growing DNA chainElongation of the growing DNA chainElongation of the growing DNA chain
The free 3'-OH group of the growing DNA chainThe free 3'-OH group of the growing DNA chain
reacts with the 5'-triphosphate of the appropriatereacts with the 5'-triphosphate of the appropriate
nucleotide.nucleotide.

Fig. 28.9 Chain elongationFig. 28.9 Chain elongationFig. 28.9 Chain elongationFig. 28.9 Chain elongation
OHOH
CHCH22
OO
OO PP
OO
O–O–
OO PP
OO
O–O–
OO PP
OO
O–O–
OO––Adenine,
Guanine,
Cytosine, or
Thymine
••••
OHOH
CHCH22OPOOPO
OO
Adenine,
Guanine,
Cytosine, or
Thymine
OO
O–O–
••••
Poly-Poly-
nucleotidenucleotide
chainchain
Poly-Poly-
chainchain

Fig. 28.9 Chain elongationFig. 28.9 Chain elongationFig. 28.9 Chain elongationFig. 28.9 Chain elongation
OHOH
CHCH22
OO
OO PP
OO––
Adenine,
Guanine,
Cytosine, or
Thymine
OO
CHCH22OPOOPO
OO
Adenine,
Guanine,
Cytosine, or
Thymine
OO
O–O–
•••• ••••
Poly-Poly-
chainchain
Poly-Poly-
chainchain
OO
OO PP
OO
O–O–
OO PP
OO
O–O–
OO––––

28.1128.11
Ribonucleic AcidsRibonucleic Acids

DNA and Protein BiosynthesisDNA and Protein BiosynthesisDNA and Protein BiosynthesisDNA and Protein Biosynthesis
According to Crick, the "central dogma" ofAccording to Crick, the "central dogma" of
molecular biology is:molecular biology is:
"DNA makes RNA makes protein.""DNA makes RNA makes protein."
Three kinds of RNA are involved.Three kinds of RNA are involved.
messenger RNA (mRNA)messenger RNA (mRNA)
transfer RNA (tRNA)transfer RNA (tRNA)
ribosomal RNA (rRNA)ribosomal RNA (rRNA)
There are two main stages.There are two main stages.
transcriptiontranscription
translationtranslation

TranscriptionTranscriptionTranscriptionTranscription
In transcription, a strand of DNA acts as aIn transcription, a strand of DNA acts as a
template upon which a complementary RNA istemplate upon which a complementary RNA is
biosynthesized.biosynthesized.
This complementary RNA isThis complementary RNA is messenger RNAmessenger RNA
(mRNA).(mRNA).
Mechanism of transcription resemblesMechanism of transcription resembles
mechanism of DNA replication.mechanism of DNA replication.
Transcription begins at the 5' end of DNA and isTranscription begins at the 5' end of DNA and is
catalyzed by the enzymecatalyzed by the enzyme RNA polymeraseRNA polymerase..

Fig. 28.10 TranscriptionFig. 28.10 TranscriptionFig. 28.10 TranscriptionFig. 28.10 Transcription
Only a section of about 10 base pairs in the DNAOnly a section of about 10 base pairs in the DNA
is unwound at a time. Nucleotides complementaryis unwound at a time. Nucleotides complementary
to the DNA are added to form mRNA.to the DNA are added to form mRNA.

The Genetic CodeThe Genetic CodeThe Genetic CodeThe Genetic Code
The nucleotide sequence of mRNA codes forThe nucleotide sequence of mRNA codes for
the different amino acids found in proteins.the different amino acids found in proteins.
There are three nucleotides per codon.There are three nucleotides per codon.
There are 64 possible combinations of A, U, G,There are 64 possible combinations of A, U, G,
and C.and C.
The genetic code is redundant. Some proteinsThe genetic code is redundant. Some proteins
are coded for by more than one codon.are coded for by more than one codon.

UUUUUU PhePhe UCUUCU SerSer UAUUAU TyrTyr UGUUGU CysCys UU
UUCUUC PhePhe UCCUCC SerSer UACUAC TyrTyr UGCUGC CysCys CC
UUAUUA LeuLeu UCAUCA SerSer UAAUAA StopStop UGAUGA StopStop AA
UUGUUG LeuLeu UCGUCG SerSer UAGUAG StopStop UCGUCG TrpTrp GG
UU
CC
AA
GG
UU
CC
AA
GG
UU
CC
AA
GG
UU CC AA GG
UU
CC
AA
GG
First letterFirst letter
Second letterSecond letter
Third letterThird letter
Table 28.3 (p 1175)Table 28.3 (p 1175)Table 28.3 (p 1175)Table 28.3 (p 1175)

UUUUUU PhePhe UCUUCU SerSer UAUUAU TyrTyr UGUUGU CysCys UU
UUCUUC PhePhe UCCUCC SerSer UACUAC TyrTyr UGCUGC CysCys CC
UUAUUA LeuLeu UCAUCA SerSer UAAUAA StopStop UGAUGA StopStop AA
UUGUUG LeuLeu UCGUCG SerSer UAGUAG StopStop UCGUCG TrpTrp GG
CUUCUU LeuLeu CCUCCU ProPro CAUCAU HisHis CGUCGU ArgArg UU
CUCCUC LeuLeu CCCCCC ProPro CACCAC HisHis CGCCGC ArgArg CC
CUACUA LeuLeu CCACCA ProPro CAACAA GlnGln CGACGA ArgArg AA
CUGCUG LeuLeu CCGCCG ProPro CAGCAG GlnGln CCGCCG ArgArg GG
AUUAUU IleIle ACUACU ThrThr AAUAAU AsnAsn AGUAGU SerSer UU
AUCAUC IleIle ACCACC ThrThr AACAAC AsnAsn AGCAGC SerSer CC
AUAAUA IleIle ACAACA ThrThr AAAAAA LysLys AGAAGA ArgArg AA
AUGAUG MetMet ACGACG ThrThr AAGAAG LysLys ACGACG ArgArg GG
GUUGUU ValVal GCUGCU AlaAla GAUGAU AspAsp GGUGGU GlyGly UU
GUCGUC ValVal GCCGCC AlaAla GACGAC AspAsp GGCGGC GlyGly CC
GUAGUA ValVal GCAGCA AlaAla GAAGAA GluGlu GGAGGA GlyGly AA
GUGGUG ValVal GCGGCG AlaAla GAGGAG GluGlu GCGGCG GlyGly GG
UU CC AA GG
UU
CC
AA
GG

UU
CC
UAAUAA StopStop UGAUGA StopStop AA
UAGUAG StopStop GG
UU
CC
AA
GG
AUUAUU IleIle ACUACU ThrThr AAUAAU AsnAsn AGUAGU SerSer UU
AUCAUC IleIle ACCACC ThrThr AACAAC AsnAsn AGCAGC SerSer CC
AUAAUA IleIle ACAACA ThrThr AAAAAA LysLys AGAAGA ArgArg AA
AUGAUG MetMet ACGACG ThrThr AAGAAG LysLys ACGACG ArgArg GG
UU
CC
AA
GG
UU CC AA GG
UU
CC
AA
GG
AUG is the "start" codon. Biosynthesis of all
proteins begins with methionine as the first amino
acid. This methionine is eventually removed after
protein synthesis is complete.
UAA, UGA, and UAG
are "stop" codons that
signal the end of the
polypeptide chain.

Transfer tRNATransfer tRNATransfer tRNATransfer tRNA
There are 20 different tRNAs, one for eachThere are 20 different tRNAs, one for each
amino acid.amino acid.
Each tRNA is single stranded with a CCA tripletEach tRNA is single stranded with a CCA triplet
at its 3' end.at its 3' end.
A particular amino acid is attached to the tRNAA particular amino acid is attached to the tRNA
by an ester linkage involving the carboxyl groupby an ester linkage involving the carboxyl group
of the amino acid and the 3' oxygen of theof the amino acid and the 3' oxygen of the
tRNA.tRNA.

Transfer RNATransfer RNATransfer RNATransfer RNA
Example—Phenylalanine transfer RNAExample—Phenylalanine transfer RNA
One of the mRNA codons for phenylalanine is:One of the mRNA codons for phenylalanine is:
UUCUUC5'5' 3'3'
AAGAAG3'3' 5'5'
The complementary sequence in tRNA is calledThe complementary sequence in tRNA is called
thethe anticodonanticodon..

Fig. 28.11 Phenylalanine tRNAFig. 28.11 Phenylalanine tRNAFig. 28.11 Phenylalanine tRNAFig. 28.11 Phenylalanine tRNA
OCCHCHOCCHCH22CC66HH55
++
NHNH33
OO
Anticodon
3'
5'
3'
5'

Ribosomal RNARibosomal RNARibosomal RNARibosomal RNA
Most of the RNA in a cell is ribosomal RNAMost of the RNA in a cell is ribosomal RNA
Ribosomes are the site of protein synthesis.Ribosomes are the site of protein synthesis.
They are whereThey are where translationtranslation of the mRNAof the mRNA
sequence to an amino acid sequence occurs.sequence to an amino acid sequence occurs.
Ribosomes are about two-thirds RNA and one-Ribosomes are about two-thirds RNA and one-
third protein.third protein.
It is believed that the ribosomal RNA acts as aIt is believed that the ribosomal RNA acts as a
catalyst—acatalyst—a ribozyme.ribozyme.

28.1228.12
Protein BiosynthesisProtein Biosynthesis

Protein BiosynthesisProtein BiosynthesisProtein BiosynthesisProtein Biosynthesis
During translation the protein is synthesizedDuring translation the protein is synthesized
beginning at its N-terminus.beginning at its N-terminus.
mRNA is read in its 5'-3' directionmRNA is read in its 5'-3' direction
begins at the start codon AUGbegins at the start codon AUG
ends at stop codon (UAA, UAG, or UGA)ends at stop codon (UAA, UAG, or UGA)

Fig. 28.12 TranslationFig. 28.12 TranslationFig. 28.12 TranslationFig. 28.12 Translation
Reaction that occurs isReaction that occurs is
nucleophilic acylnucleophilic acyl
substitution. Ester issubstitution. Ester is
converted to amide.converted to amide.
Methionine at N-terminusMethionine at N-terminus
is present as its N-formylis present as its N-formyl
derivative.derivative.

Ester at 3' end ofEster at 3' end of
alanine tRNA is Met-Ala.alanine tRNA is Met-Ala.
Process continuesProcess continues
along mRNA until stopalong mRNA until stop
codon is reached.codon is reached.

28.1328.13
AIDSAIDS

AIDSAIDSAIDSAIDS
Acquired immune deficiency syndromeAcquired immune deficiency syndrome
More than 22 million people have died fromMore than 22 million people have died from
AIDS since disease discovered in 1980sAIDS since disease discovered in 1980s
Now fourth leading cause of death worldwideNow fourth leading cause of death worldwide
and leading cause of death in Africa (Worldand leading cause of death in Africa (World
Health Organization)Health Organization)

HIVHIVHIVHIV
Virus responsible for AIDS in people is HIVVirus responsible for AIDS in people is HIV
(human immunodeficiency virus)(human immunodeficiency virus)
Several strains of HIV designated HIV-1, HIV-2,Several strains of HIV designated HIV-1, HIV-2,
etc.etc.
HIV is aHIV is a retrovirusretrovirus. Genetic material is RNA, not. Genetic material is RNA, not
DNA.DNA.

HIVHIVHIVHIV
HIV inserts its own RNA and an enzymeHIV inserts its own RNA and an enzyme
((reverse transcriptasereverse transcriptase) in T4 lymphocyte cell of) in T4 lymphocyte cell of
host.host.
Reverse transcriptase catalyzes the formation ofReverse transcriptase catalyzes the formation of
DNA complementary to the HIV RNA.DNA complementary to the HIV RNA.
HIV reproduces and eventually infects other T4HIV reproduces and eventually infects other T4
lympocytes.lympocytes.
Ability of T4 cells to reproduce decreases,Ability of T4 cells to reproduce decreases,
interfering with bodies ability to fight infection.interfering with bodies ability to fight infection.

AIDS DrugsAIDS DrugsAIDS DrugsAIDS Drugs
AZT and ddI are two drugs used against AIDSAZT and ddI are two drugs used against AIDS
that delay onset of symptoms.that delay onset of symptoms.
O
NN OO
NN33
OO
HH33CC
HOCHHOCH22
OO
NNHH
AZTAZT
O
NN
OO
HOCHHOCH22
OO
NNHH
ddIddI
NN
NN
HH
HH HH
HH

AIDS DrugsAIDS DrugsAIDS DrugsAIDS Drugs
Protease inhibitors are used in conjunction withProtease inhibitors are used in conjunction with
other AIDS drugs.other AIDS drugs.
Several HIV proteins are present in the sameSeveral HIV proteins are present in the same
polypeptide chain and must be separated frompolypeptide chain and must be separated from
each other in order to act.each other in order to act.
Protease inhibitors prevent formation of HIVProtease inhibitors prevent formation of HIV
proteins by preventing hydrolysis of polypeptideproteins by preventing hydrolysis of polypeptide
that incorporates them.that incorporates them.

28.1428.14
DNA SequencingDNA Sequencing

DNA SequencingDNA SequencingDNA SequencingDNA Sequencing
Restriction enzymes cleave the polynucleotideRestriction enzymes cleave the polynucleotide
to smaller fragments.to smaller fragments.
These smaller fragments (100-200 base pairs)These smaller fragments (100-200 base pairs)
are sequenced.are sequenced.
The two strands are separated.The two strands are separated.

Single stranded DNA divided in four portions.Single stranded DNA divided in four portions.
Each tube contains adenosine, thymidine,Each tube contains adenosine, thymidine,
guanosine, and cytidine plus the triphosphatesguanosine, and cytidine plus the triphosphates
of their 2'-deoxy analogs.of their 2'-deoxy analogs.
POCHPOCH22
OHOH
OOOO
OO
OHOH
PP
OO
OHOH
PP
OO
HOHO basebase
HHHHOO
OO

The first tube also contains the 2,'3'-dideoxy analog ofThe first tube also contains the 2,'3'-dideoxy analog of
adenosine triphosphate (ddATP); the second tube theadenosine triphosphate (ddATP); the second tube the
2,'3'-dideoxy analog of thymidine triphosphate (ddTTP),2,'3'-dideoxy analog of thymidine triphosphate (ddTTP),
the third contains ddGTP, and the fourth ddCTP.the third contains ddGTP, and the fourth ddCTP.
POCHPOCH22
OHOH
OOOO
OO
OHOH
PP
OO
OHOH
PP
OO
HOHO basebase
HHHH
OO

Each tube also contains a "primer," a shortEach tube also contains a "primer," a short
section of the complementary DNA strand,section of the complementary DNA strand,
labeled with radioactive phosphorus (labeled with radioactive phosphorus (3232
P).P).
DNA synthesis takes place, producing aDNA synthesis takes place, producing a
complementary strand of the DNA strand usedcomplementary strand of the DNA strand used
as a template.as a template.
DNA synthesis stops when a dideoxynucleotideDNA synthesis stops when a dideoxynucleotide
is incorporated into the growing chain.is incorporated into the growing chain.

The contents of each tube are separated byThe contents of each tube are separated by
electrophoresis and analyzed byelectrophoresis and analyzed by
autoradiography.autoradiography.
There are four lanes on the electrophoresis gel.There are four lanes on the electrophoresis gel.
Each DNA fragment will be one nucleotideEach DNA fragment will be one nucleotide
longer than the previous one.longer than the previous one.

Figure 27.29Figure 27.29
TT
TTGG
TTGGAA
TTGGAACC
TTGGAACCAA
TTGGAACCAATT
TTGGAACCAATTAA
TTGGAACCAATTAACC
TTGGAACCAATTAACCGG
TTGGAACCAATTAACCGGTT
ddAddA ddTddT ddGddG ddCddC
Sequence ofSequence of
fragmentfragment

Figure 27.29Figure 27.29
TT
TTGG
TTGGAA
TTGGAACC
TTGGAACCAA
TTGGAACCAATT
TTGGAACCAATTAA
TTGGAACCAATTAACC
TTGGAACCAATTAACCGG
TTGGAACCAATTAACCGGTT
ddAddA ddTddT ddGddG ddCddC
AA
AACC
AACCTT
AACCTTGG
AACCTTGGTT
AACCTTGGTTAA
AACCTTGGTTAATT
AACCTTGGTTAATTGG
AACCTTGGTTAATTGGCC
AACCTTGGTTAATTGGCCAA
fragmentfragment
original DNAoriginal DNA

28.1528.15
The Human Genome ProjectThe Human Genome Project

Human Genome ProjectHuman Genome ProjectHuman Genome ProjectHuman Genome Project
In 1988 National Research Council (NRC)In 1988 National Research Council (NRC)
recommended that the U.S. undertake therecommended that the U.S. undertake the
mapping and sequencing of the humanmapping and sequencing of the human
genome.genome.
International Human Genome SequencingInternational Human Genome Sequencing
Consortium (led by U.S. NIH) and CeleraConsortium (led by U.S. NIH) and Celera
Genomics undertook project. OrginallyGenomics undertook project. Orginally
competitors, they agreed to coordinate effortscompetitors, they agreed to coordinate efforts
and published draft sequences in 2001.and published draft sequences in 2001.

28.1628.16
DNA ProfilingDNA Profiling
and theand the
Polymerase Chain ReactionPolymerase Chain Reaction

DNA ProfilingDNA ProfilingDNA ProfilingDNA Profiling
DNA sequencing involves determining theDNA sequencing involves determining the
nucleotide sequence in DNA.nucleotide sequence in DNA.
The nucleotide sequence in regions of DNA thatThe nucleotide sequence in regions of DNA that
code for proteins varies little from one individualcode for proteins varies little from one individual
to another, because the proteins are the same.to another, because the proteins are the same.
Most of the nucleotides in DNA are inMost of the nucleotides in DNA are in
"noncoding" regions and vary significantly"noncoding" regions and vary significantly
among individuals.among individuals.
Enzymatic cleavage of DNA give a mixture ofEnzymatic cleavage of DNA give a mixture of
polynucleotides that can be separated bypolynucleotides that can be separated by
electrophoresis to give a "profile" characteristicelectrophoresis to give a "profile" characteristic
of a single individual.of a single individual.

PCRPCRPCRPCR
When a sample of DNA is too small to beWhen a sample of DNA is too small to be
sequenced or profiled, thesequenced or profiled, the polymerase chainpolymerase chain
reactionreaction (PCR) is used to make copies(PCR) is used to make copies
("amplify") portions of it.("amplify") portions of it.
PCR amplifies DNA by repetitive cycles of thePCR amplifies DNA by repetitive cycles of the
following steps.following steps.
1. Denaturation1. Denaturation
2. Annealing ("priming")2. Annealing ("priming")
3. Synthesis ("extension" or "elongation")3. Synthesis ("extension" or "elongation")

Figure 28.14 (PCR)Figure 28.14 (PCR)Figure 28.14 (PCR)Figure 28.14 (PCR)
Target regionTarget region
((aa) Consider double-stranded DNA containing) Consider double-stranded DNA containing
a polynucleotide sequence (the target region)a polynucleotide sequence (the target region)
that you wish to amplify.that you wish to amplify.
((bb) Heating the DNA to about 95°C causes the) Heating the DNA to about 95°C causes the
strands to separate. This is the denaturationstrands to separate. This is the denaturation
step.step.

((bb) Heating the DNA to about 95°C causes the) Heating the DNA to about 95°C causes the
strands to separate. This is the denaturationstrands to separate. This is the denaturation
step.step.
((cc) Cooling the sample to ~60°C causes one) Cooling the sample to ~60°C causes one
primer oligonucleotide to bind to one strand andprimer oligonucleotide to bind to one strand and
the other primer to the other strand. This is thethe other primer to the other strand. This is the
annealing step.annealing step.

((cc) Cooling the sample to ~60°C causes one) Cooling the sample to ~60°C causes one
primer oligonucleotide to bind to one strand andprimer oligonucleotide to bind to one strand and
the other primer to the other strand. This is thethe other primer to the other strand. This is the
annealing step.annealing step.
((dd) In the presence of four DNA nucleotides and) In the presence of four DNA nucleotides and
the enzyme DNA polymerase, the primer isthe enzyme DNA polymerase, the primer is
extended in its 3' direction. This is the synthesisextended in its 3' direction. This is the synthesis
step and is carried out at 72°C.step and is carried out at 72°C.

This completes one cycle of PCR.This completes one cycle of PCR.
((dd) In the presence of four DNA nucleotides and) In the presence of four DNA nucleotides and
the enzyme DNA polymerase, the primer isthe enzyme DNA polymerase, the primer is
extended in its 3' direction. This is the synthesisextended in its 3' direction. This is the synthesis
step and is carried out at 72°C.step and is carried out at 72°C.

This completes one cycle of PCR.This completes one cycle of PCR.
((ee) The next cycle begins with the denaturation) The next cycle begins with the denaturation
of the two DNA molecules shown. Both areof the two DNA molecules shown. Both are
then primed as before.then primed as before.

((ee) The next cycle begins with the denaturation) The next cycle begins with the denaturation
of the two DNA molecules shown. Both areof the two DNA molecules shown. Both are
then primed as before.then primed as before.
((ff) Elongation of the primed fragments completes) Elongation of the primed fragments completes
the second PCR cycle.the second PCR cycle.

((ff) Elongation of the primed fragments completes) Elongation of the primed fragments completes
the second PCR cycle.the second PCR cycle.
((gg) Among the 8 DNAs formed in the second) Among the 8 DNAs formed in the second
cycle are two having the structure shown.cycle are two having the structure shown.

The two contain only the target region andThe two contain only the target region and
and are the ones that increase disproportionatelyand are the ones that increase disproportionately
in subsequent cycles.in subsequent cycles.
((gg) Among the 8 DNAs formed in the second) Among the 8 DNAs formed in the second
cycle are two having the structure shown.cycle are two having the structure shown.

Dr. Wolf's CHM 424 28- 100
CycleCycle Total DNAsTotal DNAs Contain only targetContain only target
0 (start)0 (start) 11 00
11 22 00
22 44 00
33 88 22
44 1616 88
55 3232 2222
1010 1,0241,024 1,0041,004
2020 1,048,5661,048,566 1,048,5261,048,526
3030 1,073,741,8241,073,741,824 1,073,741,7641,073,741,764

Dr. Wolf's CHM 424 28- 101
End of Chapter 28End of Chapter 28

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