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and RNA molecules of hered

Lecture
16 November – 7 December
2009
INFORMATION PATHWAYS
The fundamental unit of
information in living systems is
the gene.
A gene can be defined
biochemically as a segment
of DNA (or, in a few cases, RNA)
that encodes the information
required to produce a functional
biological product.
The final product is usually a
protein.
Today’s understanding of information
pathways has arisen from the
convergence of genetics, physics,
and chemistry in modern
biochemistry.
This was epitomized by the discovery
of the double-helical structure of
DNA, postulated by James Watson
and Francis Crick in 1953.
Genetic theory contributed the
concept of coding by genes.

These and other major advances gave
rise to the central dogma of
molecular biology, comprising the
three major processes in the cellular
utilization of genetic information.
The first is replication, the copying of
parental DNA to form daughter DNA
molecules with identical nucleotide
sequences.
The second is transcription, the
process by which parts of the genetic
message encoded in DNA are copied
precisely into RNA.
The third is translation, whereby the
The double-helical structure itself
clearly suggested how DNA might
be copied so that the information it
contains can be transmitted from
one generation to the next.
Clarification of how the information in
DNA is converted into functional
proteins came with the discovery of
both messenger RNA and transfer
RNA and with the deciphering of the
genetic code.
Figure 1. The central dogma of molecular genetics.
The flow of genetic information via the three
fundamental processes of replication, transcription,
and translations.
DNA: deoxyribonucleic acid
DNA is a polymer of
deoxyribonucleotide units.
DNA functions to store the
complete genetic information
required to specify the structure
of all the proteins.
RNA: ribonucleic acids
RNA consist of long strings of
ribonucleotides.
RNAs functions to program the
orderly biosynthesis of cell and
tissue component
Nucleotides:
Biological molecules that possess
heterocyclic nitrogenous bases as
The biochemical
principal roles;of their
components
participate
structure. as essential
intermediates in all aspects of
cellular metabolism.
N ucleic acids:
The elements of heredity and the
agents
Linear of geneticofinformation
polymers nucleotides.
transfer.
Like the letters in this sentence,
the orderly sequence of nucleotide
residues in a nucleic acid can
encode information.
The two basic kinds of nucleic acids
are:
- deoxyribonucleic acid (DNA)
- ribonucleic acid (RNA).
Complete hydrolysis of nucleic acids
liberates: nitrogenous bases, a five-
carbon sugar, and phosphoric acid in
equal amounts.
The five-carbon sugar in:
- DNA is 2-deoxyribose;
- RNA is ribose.
DNA is the repository of genetic
information in cells.

RNA serves in the transcription


and translation of this
information (Figure 1).
An interesting exception to this
rule is that some viruses have
their genetic information stored
as RNA.
FIGURE 2● The
fundamental
process of
information
transfer in cells .
Replication
DNA replication yields two DNA molecules
identical to the original one, ensuring
transmission of genetic information to daughter
cells with exceptional fidelity.
Transcription
The sequence of bases in DNA is recorded as a
sequence of complementary bases in a
singlestranded mRNA molecule.
Translation
Three-base codons on the mRNA corresponding to
specific amino acids direct the sequence of
building a protein. These codons are recognized
by tRNAs (transfer RNAs) carrying the
appropriate amino acids. Ribosomes are the
“machinery” for protein synthesis.
Figure 2 ● The fundamental process of
information transfer in cells.
Information encoded in the nucleotide
sequence of DNA is transcribed through
synthesis of an RNA molecule whose
sequence is dictated by the DNA sequence.
As the sequence of this RNA is read (as
groups of three consecutive nucleotides)
by the protein synthesis machinery, it is
translated into the sequence of amino
acids in a protein.
This information transfer system is
encapsulated in the dogma: DNA  RNA 
protein.
The Nucleotide units of DNA and
RNA Have Characteristic Bases
and Pentoses
Nucleotides contain three
characteristic components:
◦ (1) a nitrogenous base;
◦ (2) a pentose;
◦ (3) phosphoric acid

•T h e b a se is co va le n tly jo in e d in a n N -
g lyco syllin ka g e to ca rb o n a to m 1 ’ o f th e
p e n to se a n d th e p h o sp h o ric a cid is
e ste rifie d to ca rb o n 5 ’.
Purine or
Phosphoester bond pyrimidine
base

O- 5’
- O- O β
CH 2
Phosphat| 4’ 1’
e O– – P H H
Pentose
H H
||
3’ 2’
OH
O-
OH
Table 1 . The principal pyrimidine
and purine bases of DNA and RNA

DNA RNA
Purines Adenine Adenine
Guanine Guanine
Pyrimidines Cytosine Cytosine
Thymine Uracil
Nitrogenous Bases

Pyrimidine Purine ring


ring
Figure 3 ● ( a ) The pyrimidine ring
system ; by convention, atoms are numbered as
indicated.
(b) The purine ring system, atoms numbered
The common pyrimidine

Cytosine Uracil Thymine


( 2 - oxy - 4 - ( 2 - oxy - 4 - oxy ( 2 - oxy - 4 - oxy
amino pyrimidine ) 5 - methyl
pyrimidine ) pyrimidine )
The common purine

Adenine Guanine
( 6 - amino ( 2 - amino - 6 - oxy
purine ) purine )
The Pentoses of Nucleotides and
Nucleic Acids

Figure 5 ● Furanose structures


— ribose and deoxyribose .
Nucleosides Are Formed by Joining
Nucleosides
a Nitrogenous areBase
compounds formed when
to a Sugar
In nucleosides,
a base is linked the
to abond
sugarisvia
an aN-glycoside
glycosidic
because
bond. it connects the anomeric C-1 to N-
1 of a pyrimidine or to N-9 of a purine.
ds link nitrogenous bases and sugars to f

β- N1 - glycosidic β- N9 - glycosidic
bond in pyrimidine bond in purine
ribonucleosides ribonucleosides
Glycosidic bonds in nucleosides and
nucleotides are always of the β-
configuration,
Nucleosides are named by adding the
ending –idine to the root name of a
pyrimidine or -osine to the root name of a
purine.
The common nucleosides are thus cytidine,
uridine, thymidine, adenosine, and
guanosine.
The common ribonucleosides—
cytidine, uridine, adenosine, and
guanosine.
Cytidine Uridine

Adenosine Guanosine
Nucleotides Are Nucleoside Phosphates
A nucleotide results when phosphoric acid is
esterified to a sugar -OH group of a nucleoside.

Adenosine 5' - monophosphate


( or AMP or adenylic acid )
Structures of the four common
ribonucleotides—AMP, GMP, CMP, and
UMP

Adenosine 5' -
monophosphate
( or AMP or adenylic
acid )
Guanosine 5' -
monophosphate
( or GMP or guanylic acid )
Cytidine 5' -
monophosphate
( or CMP or cytidylic
acid )

Uridine 5' -
monophosphate
( or UMP or uridylic
acid )
Table 2 . Nucleotide and Nucleic
Acid Nomenclature

Base
Purines
Pyrimidines
Adenine
Guanine
Cytosine
Thymine
Uracil Uridine
Nucleoside
Adenosine
Deoxyadenosine
Guanosine
Deoxyguanosine
Cytidine
Deoxycytidine
Thymidine or Uridylate
Nucleotide
Adenylate
Deoxyadenylate
Guanylate
Deoxyguanylate
Cytidylate
Deoxycytidylate
Thymidylate or Nucleic
RNA
DNA
deoxythymidine deoxythymidylate acid
FIGURE 7 . Deoxyribonucleotides and ribonucleotides of nucleic acids .
All nucleotides are shown in their free form at pH 7.0.
Phosphodiester Bonds Link the
Successive Nucleotides of
Nucleic Acids
• The phosphodiester bonds (one of
which is shaded in the DNA) link
successive nucleotide units.
• The backbone of alternating pentose
and phosphate groups in both
types of nucleic acid is highly polar.
• The 5 end of the macromolecule
lacks a nucleotide at the 5 position,
and the 3 end lacks a nucleotide at
the 3 position.
FIGURE 8 – 7
Phosphodiester
linkages in the
covalent backbone of
DNA and RNA .

3’-5’ phosphodiester
bridges link nucleotides
together to form
polynucleotide chains
Nucleic Acids Are
Nucleic acids are linear polymers of nucleotides
Polynucleotides
They
linkedare
3’formed
to 5’ byasphosphodiester
5’-nucleoside monophosphates
bridges are
Polymers of ribonucleotides
successively are named
added to the 3’-OH ribonucleic
group of the preceding
Deoxyribonucleotide
acid, or RNA.
nucleotide, polymers
a process that arepolymer
gives the called a directional
deoxyribonucleic
sense. acid, or DNA.
Figure: 3’-5’
phosphodiester
bridges link
nucleotides
together to
form
polynucleotide
chains.
Shorthand Notations for
The convention in all notations of
Polynucleotide
To distinguish
nucleic Structures
between
acid structure RNAtoand
is DNAthe
read
sequences , DNA sequences
polynucleotide chain fromare thetypically
5’-end of
preceded
the polymerby atolowercase
the 3’-end“. dNote
” to denote
that this
deoxy , asdirection
reading in d-GACGTA
actually
. passes through
each phosphodiester from 3’ to 5’.
Furanoses are represented by lines; phosphodiesters are
represented by diagonal slashes in this shorthand
notation for nucleic acid structures.
Classes of Nucleic Acids
The two major classes of nucleic acids
DNA
are has
DNA only one. biological role, but it
and RNA
The information
is the to make
more central one. all the
functional macromolecules of the cell
(even DNA itself) is preserved in DNA
and accessed through transcription of
the information into RNA copies.
Coincident with its singular purpose, there is only a single
Such
DNA DNA molecules
molecule must be quitein
(or “chromosome”) large in order
simple to
life forms
The
suchEscherichia
embrace enoughorcoli
as viruses chromosome
information
bacteria. has a molecular
for making the mass of
Eukaryotic
2.9 x 109 Dcells have many
and contains
macromolecules necessary tochromosomes,
over and cell.
DNA is
9 millionanucleotides.
maintain living
found principally in two copies in the diploid chromosomes
of the nucleus, but it also occurs in mitochondria and in
chloroplasts, where it encodes some of the proteins and
RNAs unique to these organelles
In contrast, RNA occurs in multiple copies and
Cells contain
various formsup . to eight times as much RNA as
RNA
DNA.has a number of important biological
Eukaryotic
functions, andcells
on contain anRNA
this basis, additional type,are
molecules
small nuclear
categorized intoRNA (snRNA).
several major types: messenger
RNA (mRNA), ribosomal RNA (rRNA), and
transfer RNA (tRNA)
chromosomes
Chromosomes are composed of chromatin
Chromatin
and carry consists
the gene of in protein
a linear sequence;
Gene isdetermine
a unit
principally
(these oftheheredity
histones ), DNA, composed
and smallof
individual
DNA
amounts
. of RNA of an organism.
characteristics
Mendel’s laws: A gene is visualized as
a particle, forming part of a
chromosome, that determines a particular
characteristic.
DNA
The DNA isolated from different cells and
The strands
viruses run in oppositeconsists
characteristically directionsof; twothat
These
is , theyH bonds
polynucleotide pair the bases
are antiparallel
strands and of
wound arenucleotides
held to
together
together
in in, the
formonea chain
long double helicalmolecule
to complementary
slender , helical structure
bases in, the
the
other
through, a interchain
DNA double helix. hydrogen
phenomenon bonds
called base pairing
. .
The antiparallel nature of the DNA
double helix.
Chargaff ’ s Rules
A clue to the chemical basis of base
The baseincomposition
pairing DNA came fromof DNA
thegenerally
analysis of
DNA
the specimens
varies isolatedoffrom
base composition different
various DNAs by
tissues
from
Erwinone ofspeciesintotheanother
Chargaff late 1940s
. .
the same species have the same base
composition.
Chargaff ’ s Rules
The base composition of DNA in a given
His data showed that the four bases
species
commonly
does not found
changeinwith
DNAan(A,organism
C, G, and
’s Tage
) do
,
not occur instate
nutritional equimolar amounts and that
, or changing
the relative. amounts of each vary from
environment
species to species
Chargaff ’ s Rules
Chargaff noted that certain pairs of
These
bases, findings are known
namely, adenine Chargaff
andasthymine ’s
, and
rules
guanine
: and cytosine, are always found in
a 1:1 ratio and that the number of
[A] =residues
pyrimidine [T]; [C] = [G]; [pyrimidines
always equals the ] =
purinesof
[number ]. purine residues.
Watson and Crick ’ s Double Helix
James Watson and Francis Crick, working in the
Cavendish
Two strandsLaboratory at Cambridgeacid
of deoxyribonucleic University
are held
in 1953, took
together advantage
by hydrogen of Chargaff
bonds ’s results
formed between
and thebase
unique datapairs
obtained by Rosalind
, always Franklin
consisting of a and
MauriceinWilkins
purine in X-ray
one strand and diffraction
a pyrimidinestudies
in the on
the structure of DNA to conclude that DNA was
other
a complementary double
helix.
Rosalind Franklin,
1920–1958

Figure . The x-ray diffraction


pattern of DNA. The spots forming
across in the center denote a
helical structure. The heavy
bands at the left and right
correspond to the recurring bases
Maurice Wilkins
Base pairing is very specific: if the
Tpurine
hese pairs are taken
is adenine , the as the standard
pyrimidine must or
accepted
be thyminelaw , and the, AT
. Similarly and GCpairs
guanine base only
pairs are often referred to as
with cytosine.
canonical. A : T and G : C

James Watson Francis Crick


The Watson – Crick base pai

G : C

A :
T
Figure 5 . 11 . Watson - Crick Model of Double - Helical DNA .
One polynucleotide chain is shown in blue and the other in red.
The purine and pyrimidine bases are shown in lighter colors than
the sugar-phosphate backbone. (A) Axial view. The structure
repeats along the helical axis (vertical) at intervals of 34 Å,
which corresponds to 10 nucleotides on each chain.
(B) Radial view, looking down the helix axis.
The DNA Double Helix Is a Stable Structur
Several factors account for the stability of the
1double-helical
) First structureand
, both internal of external
DNA. hydrogen
bonds stabilize the double helix.
The two strands of DNA are held together by H-
bonds that form between the complementary
purines and pyrimidines, two in an A : T pair and
three in a G:C pair,
while polar atoms in the sugar–phosphate
backbone
form external H bonds with surrounding water
molecules.
2) The negatively charged phosphate groups are
3all situated
) The core ofonthe
thehelix
exterior surface
consists of the
of the base
helix, in
pairs such
which, ina addition
way that to
they haveHbonded
being minimal
,
effecttogether
stack on one another
throughand are free to
hydrophobic interact
interactions
electrostatically
and with cations
van der Waals forces in solution such
that contribute
as Mg2.
significantly to the overall stabilizing
energy.
Figure 5 . 13 . Axial View of DNA . Base pairs are
stacked nearly one on top of another in the double
helix.
FIGURE 11 . 21 ●
Replication of DNA
gives identical
progeny molecules
because base pairing
is the mechanism
determining the
nucleotide sequence
synthesized within
each of
the new strands during
replication.
Denaturation and Renaturation of DNA
Thermal Denaturation and
When duplex DNA molecules
Hyperchromic Shift are subjected
That is, the double
to conditions of pH,helix is denatured
temperature , or
If
and temperature
ionic strandsis
thestrength thedisrupt
separate
that denaturing agent,
as hydrogen
individual
the
bondsdouble
random helix
coils
, the strands
. isare
said
no to melt.held
longer
Together.
The rise in absorbance (λ 269 nm) coincides
The
withhigher
strandthe G : C content
separation of midpoint
, and the a DNA, theof
Tm
theisabsorbance
higher dependent
its meltingon the ionic
temperature
increase strength
is termed the ofG the
because : C
DNA
pairsinare
solution
melting purethewater
held by melts
lower
;temperature ,the even
Tm. ionic
three at
H bonds room
strength
whereas, the
A :T
temperature
lower
pairs the
havemelting
.only twotemperature
. .
Heat denaturation of DNA .
( a ) The denaturation , or melting, curves of two DNA
specimens. The temperature at the midpoint of the
transition (tm) is the melting point; it depends on pH
and ionic strength and on the size and base
composition of the DNA.
( b ) Relationship between tm and the G: C content
of a DNA .
trong H - Bonding Solutes Also Denatu

At pH values greater than 10 , extensive


Edeprotonation of the
xtensive protonation of bases occurs
the bases below
, pH 2.3
destroying
disrupts
Alkali thetheir
isbase hydrogen
pairing
preferred bonding
. denaturant because,
potential
unlike acid, and denaturing
it does the DNA
not hydrolyze the duplex .
glycosidic linkages in the sugar–phosphate
backbone.
DNA Renaturation
Denatured DNA will renature to re-form
That is, if structure
the duplex the solution is cooled
if the , the pH
denaturing
Renaturation
is returnedare
conditions requires
to reassociation
neutrality
removed . , or the of
the DNA strands
denaturants are into a double
diluted out helix, a
process termed reannealing.
For this to occur, the strands must
Renaturation is dependent
realign themselves so thatboth
theiron DNA
concentration
complementary and time. Many of the
realignments
bases are onceareagain
imperfect , and thus
in register and the
the
strands
helix canmust
be dissociate
zippered upagain to allow
for proper pairings to be formed.
Steps in the thermal denaturation and renaturation of DNA. The
nucleation phase of the reaction is a second-order process depending
on sequence alignment of the two strands. This process takes place
slowly because it takes time for complementary
sequences to encounter one another in solution and then align
themselves in register.
Once the sequences are aligned, the strands zipper up quickly.
DNA Strands from Two Different
Species Can Form DNA-DNA Hybrids
The ability of two complementary DNA
strands to pair with one another can
be used to detect similar DNA
sequences in two different species or
within the genome of a single
species.
The closer the evolutionary
relationship between two species, the
more extensively their DNAs will
hybridize.
For example, human DNA hybridizes
much more extensively with mouse
Sample 1 Sample 2

Mix and
cool

Duplex of
sample 1

Hybrid Duplex of
Duplex sample 2
Chromosomes contain structural
genes and regulatory sequences
Genes that code for polypeptides
and RNAs are known as structural
genes.
They determine the structure of
some final gene product, such as an
enzyme or RNA.
DNA also contains regulatory
segments that:
• Constitute signals denoting the
beginning and end of structural
genes;
There are many genes in a single
chromosome
Figure 6.6. A Complete Genome.
The diagram depicts the genome of
Haemophilus influenzae, the first
complete genome of a free-living
organism to be sequenced.
The genome encodes more than
1700 proteins and 70 RNA
molecules.
The likely function of approximately
one-half of the proteins was
determined by comparisons with
DNA RNA Polypeptide
Figure 27-27 . Colinearity 5’ 3’ 5’ Amino
| | | terminal
of the nucleotide sequences C G C end
of between DNA, mRNA, and G C G |
T A U Arginine
the amino acid sequence of G C G
polypeptide chains. The G
A
C
T
G
A
triplets of nucleotide T A U Glycine
units in DNA determine the A
C
T
G
A
C
sequence of amino acids in A T A Tyrosine
proteins through the C
T
G
A
C
U
intermediary formation of T A U Threonine
mRNA, which has nucleotide T
T
A
A
U
U
triplets (codons) G C G Phenylalanin
e
complementary to those of a C
C
G
G
C
C
DNA template strand | | |
3’ 5’ 3’ Alanine
|
Carboxyl
terminal End

The complementary
strand

The coding strand


Other Functions of
Nucleotides
Inaddition to their roles as the
subunits of nucleic acids,
nucleotides have a variety of
other functions in every cell as:
• energy carriers
• components of enzyme
cofactors,
• and chemical messengers.

Nucleotides Carry
Chemical Energy in Cells
The phosphate group covalently
linked at the 5 hydroxyl of a
ribonucleotide may have one or
two additional phosphates
attached.
The resulting molecules are
referred to as nucleoside mono-,
di-, and triphosphates
(Fig. ).

FIGURE 8 – 39 Nucleoside phosphates .
General structure of the nucleoside 5-mono-, di-,
and triphosphates (NMPs, NDPs, and NTPs) and their
standard abbreviations. In the
deoxyribonucleoside phosphates (dNMPs, dNDPs, and
dNTPs), the pentose is 2-deoxy-D-ribose.
Formation of ADP and ATP by the successive
addition of phosphate groups via
phosphoric anhydride linkages
Triphosphates Are Carriers of Ch
Nucleoside 5 ’- triphosphates are
ATP has been termed
indispensable the energy
agents currency of
in metabolism
GTP
the is the
cell
because major
. the energy source
phosphoric for protein
anhydride
synthesis
bonds they possess are a prime
source of chemical energy to do
biological work .
CTP is an essential metabolite in
UTP forms activated
phospholipid intermediates with
synthesis
The evolution
sugars that goofonmetabolism
to serve as hassubstrates
led to the
To
in complete
dedication theone
of picture
the biosynthesis , thefour
ofofthese
complexfourNTPs
NTPstoand
their
each ofdNTP
thecounterparts
carbohydrates major
and branchesareofthemetabolism
polysaccharides substrates
.
for the synthesis of the remaining great
class of biomolecules—the nucleic acids.
Adenine Nucleotides Are
Components of Many Enzyme
Cofactors
Coenzyme A (CoA) functions in acyl
group transfer reactions.
NAD functions in hydride transfers.
FAD, the active form of vitamin B2
(riboflavin), in electron transfers.
5-deoxyadenosylcobalamin, the
active form of vitamin B12 , which
participates in intramolecular
group transfers between adjacent
carbons.

Some Nucleotides Are
Regulatory Molecules
Cells respond to their environment
by taking cues from hormones or
other external chemical signals.
The interaction of these
extracellular chemical signals
(“first messengers”) with
receptors on the cell surface often
leads to the production of second
messengers inside the cell,
which in turn leads to adaptive
changes in the cell interior.
One of the most common is
adenosine 3,5-cyclic
monophosphate (cyclic AMP, or
cAMP), formed from ATP in a
reaction catalyzed by adenylyl
cyclase, an enzyme associated with
the inner face of the plasma
membrane.
Cyclic AMP serves regulatory
functions in virtually every cell
outside the plant kingdom.
Guanosine 3,5-cyclic monophosphate
(cGMP) occurs in many cells and

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