LECTURE 13-15

Composition of DNA and RNA, simple structure

Replication, transcription and translation

Maj Md. Ashrafuzzaman, Ph.D, EME

 o n
t s Cr
a ick
W
DNA

DNA stands for deoxyribose nucleic acid

This chemical substance is present in the nucleus

of all cells in all living organisms
DNA controls all the chemical changes which
take place in cells
The kind of cell which is formed, (muscle, blood,
nerve etc) is controlled by DNA
DNA molecule

DNA is a very large molecule made up of a long

chain of sub-units
The sub-units are called nucleotides

Each nucleotide is made up of

a sugar called deoxyribose
a phosphate group -PO4 and
an organic base
28.8 Nucleic Acids and Nucleotides
 Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA),
are the chemical carriers of genetic information
 Nucleic acids are biopolymers made of nucleotides,
aldopentoses linked to a purine or pyrimidine and a
phosphate

5 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
Heterocycles in DNA and RNA

 Adenine, guanine, cytosine and thymine are in DNA

 RNA contains uracil rather than thymine

Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
Deoxyribonucleotides found in
DNA

dA dG dT dC
The Deoxyribonucleotides

8
 Hydrogen Bonding Interactions

 Two bases can hydrogen bond to form a base pair

 For monomers, large number of base pairs is
possible
 In polynucleotide, only few possibilities exist
 Watson-Crick base pairs predominate in double-
stranded DNA
 A pairs with T
 C pairs with G
 Purine pairs with pyrimidine
一、 thebuilding block molecule of
nucleic acid--nucleotide

In RNA:
AMP 、 CMP 、 GMP 、 TMP
In DNA:
dAMP 、 dCMP 、 dGMP 、 dUMP
 Functions of
Nucleotides and Nucleic Acids
 Nucleotide Functions:
 Energy for metabolism (ATP)
 Enzyme cofactors (NAD+)
 Signal transduction (cAMP)

 Nucleic Acid Functions:

 Storage of genetic info (DNA)
 Transmission of genetic info (mRNA)
 Processing of genetic information (ribozymes)
 Protein synthesis (tRNA and rRNA)
 DNA Nucleotides
Composition (3 parts):
1- Deoxyribose sugar (no O in 3rd carbon)
2- Phosphate group
3- One of 4 types of bases (all containing
nitrogen):
- Adenine
- Thymine (Only in DNA)
- Cytosine
- Guanine
28.10 Base Pairing in DNA: The Watson–
Crick Model
 In 1953 Watson and Crick noted that DNA consists of
two polynucleotide strands, running in opposite
directions and coiled around each other in a double
helix
 Strands are held together by hydrogen bonds between
specific pairs of bases
 Adenine (A) and thymine (T) form strong hydrogen
bonds to each other but not to C or G
 (G) and cytosine (C) form strong hydrogen bonds to
each other but not to A or T

Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
The Difference in the Strands
 The strands of DNA are
complementary because of H-
bonding
 Whenever a G occurs in one strand,
a C occurs opposite it in the other
strand
 When an A occurs in one strand, a T
occurs in the other

Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
 Primary Structure of Nucleic Acids
 The primary structure of a nucleic acid is the nucleotide sequence
 The nucleotides in nucleic acids are joined by phosphodiester bonds
 The 3’-OH group of the sugar in one nucleotide forms an ester bond
to the phosphate group on the 5’-carbon of the sugar of the next
nucleotide
Generalized Structure of DNA

17
 Reading Primary Structure

 A nucleic acid polymer has a free 5’-

phosphate group at one end and a
free 3’-OH group at the other end
 The sequence is read from the free
5’-end using the letters of the bases
 This example reads
5’—A—C—G—T—3’
Example of DNA Primary Structure
 In DNA, A, C, G, and T are linked by 3’-5’ ester bonds
between deoxyribose and phosphate
 Nucleic Acid Structure
Polymerization

Nucleotide
Sugar Phosphate
“backbone”
Describing a Sequence

 Chain is described from 5 end,

identifying the bases in order of
occurrence, using the abbreviations A
for adenosine, G for guanosine, C for
cytidine, and T for thymine (or U for
uracil in RNA)
 A typical sequence is written as
TAGGCT
Based on McMurry, Organic Chemistry,
Chapter 28, 6th edition, (c) 2003
Properties of a DNA
double helix

The strands of DNA are antiparallel

The strands are complimentary

There are Hydrogen bond forces

There are base stacking interactions

There are 10 base pairs per turn

 The Double Helix (DNA)
Structural model:
 Model proposed by Watson & Crick, 1953
 Two sugar-phosphate strands, next to each
other, but running in opposite directions.
 Specific Hydrogen bonds occur among bases
from one chain to the other:
A---T , C---G
Due to this specificity, a certain base on one
strand indicates a certain base in the other.
 The 2 strands intertwine, forming a double-
helix that winds around a central axis
 • The sides of the ladder are:
Untwisted it
P = phosphate
looks like this: S = sugar molecule
• The steps of the ladder are C, G, T, A =
nitrogenous bases
(Nitrogenous means containing the
element nitrogen.)

A = Adenine (Apples are Tasty)

T = Thymine
A always pairs with T in DNA

C = Cytosine (Cookies are Good)

G = Guanine
Nucleotide C always pairs with G in DNA
 Secondary Structure: DNA Double Helix
 In DNA there are two strands of nucleotides that wind together
in a double helix
- the strands run in opposite directions
- the bases are are arranged in step-like pairs
- the base pairs are held together by hydrogen bonding
 The pairing of the bases from the two strands is very specific
 The complimentary base pairs are A-T and G-C
- two hydrogen bonds form between A and T
- three hydrogen bonds form between G and C
 Each pair consists of a purine and a pyrimidine, so they are the
same width, keeping the two strands at equal distances from
each other
Model of DNA:
• The model was developed
by Watson and Crick in
1953.

• They received a nobel prize

in 1962 for their work.

• The model looks like a

twisted ladder – double
helix.
 Nucleic Acid Structure
“Base Pairing”
DNA base-pairing is antiparallel
i.e. 5’ - 3’ (l-r) on top : 5’ - 3’ (r-l) on

5’ 3’

T A G C A C
A T C G T G

3’ 5’
Discovering the structure of DNA

Erwin Chargaff – (1905-2002)

• Columbia University, NY
• Investigated the composition of DNA
• His findings by 1950 strongly
suggested the base-pairings
of A-T & G-C
• Met with Watson and Crick in
1952 and shared his findings
• “Chargaff’s rule” A = T & C = G
 Nucleic Acid Structure
The double helix
First determined by Watson & Crick in 1953

Most energy favorable conformation for double stranded DNA to

form
Shape and size is uniform for all life (i.e. DNA is identical)

Without anti-parallel base pairing this conformation could

not exist
Structure consists of “major” grooves and “minor” grooves

Major grooves are critical for binding proteins that regulate DNA
function
Discovering the structure of DNA

• DNA = Deoxyribose nucleic acid

• Present in all living cells
• Contains all the information
• Nucleotides:

• a subunit that consists of:

• a sugar (deoxyribose)
• a phosphate
• and one nitrogen base – 4 different bases
• Adenine (A) and Thymine (T)
• Guanine (G) and Cytosine (C)
The paired strands are coiled into a spiral called

A DOUBLE HELIX
 PO4
PO4 The strands
separate PO4
PO4

PO4 PO4

PO4 PO4

PO4
PO4

PO4
PO4

PO4
PO4

PO4
PO4
 Nucleic Acid Structure
“Base Pairing”
RNA [normally] exists as a single stranded polymer
DNA exists as a double stranded polymer

DNA double strand is created by hydrogen bonds between

nucleotides
Nucleotides always bind to complementary nucleotides

A T (2 H-bonds)

G C (3 H-bonds)
Practice DNA Base Pairs

GATTACA
C T AA T G T
Nucleic Acid Structure
The double helix

Minor
Groove

Major
Groove
replication

Before a cell divides, the DNA strands unwind

and separate
Each strand makes a new partner by adding
the appropriate nucleotides
The result is that there are now two
double-stranded DNA molecules in the
nucleus
So that when the cell divides, each nucleus
contains identical DNA
This process is called replication
 STEP 1
Hydrogen bonds between DNA molecule
base pairs are broken by the separates into
enzyme Helicase and DNA complementary halves
molecule unzips
Complementarity of DNA strands

 Two chains differ in sequence

(sequence is read from 5’ to 3’)
 Two chains are complementary
 Two chains run antiparallel
Nucleic Acid Structure
“Base Pairing”
 Nucleic Acid Structure
Polymerization

5’ 3’
Sugar Phosphate
“backbone”

T A G C A C
Bases

5’ 3’
TAGCAC
 Nucleic Acid Structure
Polymerization

P P P P P P
N N
C C
S Phosphodiesterase S

+
P
N
P P
C
(PPi)
S
P P P
N
C
S
DNA Replication
• Cell division involving mitosis produces 2 daughter
cells that are genetically identical to each other and
genetically identical to the parent cell
• Remember that for this to happen, DNA in the parent
cell must be replicated (copied) before the cell divides
– this process occurs during Interphase in the cell
cycle
 STEP 2
Nucleotides match up with
complementary bases

Free nucleotides abundant in nucleus

 STEP 3
Nucleotides are linked into 2 new strands of DNA by
the enzyme, polymerase—DNA polymerase also
proofreads for copying errors

New Strand
Original Strand
Mutations occur when
copying errors cause a
change in the sequence of
DNA nucleotide bases
Diagram Examples of DNA Replication:
(You could see DNA replication represented different ways.)
 Storage of DNA
 In eukaryotic cells (animals, plants, fungi) DNA is stored in
the nucleus, which is separated from the rest of the cell by a
semipermeable membrane
 The DNA is only organized into chromosomes during cell
replication
 Between replications, the DNA is stored in a compact ball
called chromatin, and is wrapped around proteins called
histones to form nucleosomes
 DNA Replication
 When a eukaryotic cell divides, the process is called mitosis
- the cell splits into two identical daughter cells
- the DNA must be replicated so that each daughter cell has a copy
 DNA replication involves several processes:
- first, the DNA must be unwound, separating the two strands
- the single strands then act as templates for synthesis of the new
strands, which are complimentary in sequence
- bases are added one at a time until two new DNA strands that
exactly duplicate the original DNA are produced
 The process is called semi-conservative replication because one
strand of each daughter DNA comes from the parent DNA and one
strand is new
 The energy for the synthesis comes from hydrolysis of phosphate
groups as the phosphodiester bonds form between the bases
 Figure 5-14 Schematic representation of the strand
separation in duplex DNA resulting from its heat
denaturation.
Page 90
 Direction of Replication
 The enzyme helicase unwinds several sections of parent DNA
 At each open DNA section, called a replication fork, DNA
polymerase catalyzes the formation of 5’-3’ester bonds of the
leading strand
 The lagging strand, which grows in the 3’-5’ direction, is
synthesized in short sections called Okazaki fragments
 The Okazaki fragments are joined by DNA ligase to give a single
3’-5’ DNA strand
 In cells, when DNA is going to be replicated, a section of the
double helix called the “origin” is opened up, and a special
RNA polymerase called “primase” makes an RNA primer
molecule complementary to the DNA template.

This RNA
stays bound to
the DNA
template, and
serves as a RNA primer Origin primer

primer, to be
elongated by
DNA
polymerase.
Origin primer

RNA primer
at origin

61
A protein complex called “helicase” opens up the double
stranded DNA at the origin, and then runs along the DNA at
the replication fork, continuing to open up the double helix.
Meanwhile, an enzyme called “topoisomerase” runs ahead of
the replication fork, relieving the strain on the double helix
created by the unwinding action of helicase.

5’

And many copies of a protein called “single-stranded DNA

binding protein” bind the separated strands to keep then single-
stranded
62
 After the primer has been synthesized, DNA polymerase
(“Pol III”) adds dNTPs to the 3’ end of the RNA primer, and
synthesizes DNA along the template strand, moving in a 5’ to
3’ direction. It can continue in this fashion until it reaches
the 5’ end of the template strand, and the daughter strand
that is synthesized is called the “leading strand”.

“Leading strand”
Topoisomerase

Helicase

63
Now consider replication off the other strand of
the parent DNA molecule; ie, synthesis of the
“lagging strand”:
(Ongoing synthesis of the leading strand.)

Pol III
Topoisomerase

5’
3’

Helicase

RNA primer for

synthesis of lagging
strand of DNA

As before, primase initiates

synthesis of the lagging strand by
creating an RNA primer on the
template strand.
64
A theoretical (but incorrect) model for DNA
replication:

Leading strand, growing in

5’ to 3’ direction.

Hypothetical 3’ to 5’
growth of the other
strand

If one daughter strand could grow 3’ to 5’, while the other strand
is growing 5’ to 3’, then both daughter strands could grow
continuously towards the ends of the two template strands.

65
But, for reasons having largely to do with error
correction mechanisms, a 3’ to 5’ DNA polymerase
has never evolved; all DNA polymerases found in
nature can only elongate DNA in a 5’ to 3’ direction.

(Each Okazaki fragment begins with a

section of RNA primer at it’s 5’ end)

This means that synthesis of the lagging strand must

be discontinuous. The discontinuously synthesized
fragments of DNA are called “Okazaki fragments”.
66
Here’s how your book presents the situation
with synthesis of the lagging strand:

67
Details on the synthesis of the lagging strand:
Pol III

Topoisomerase

Helicase

Pol III

Topoisomerase

Helicase
(Yellow = RNA; Red = DNA)

Pol III

Topoisomerase

5’

Pol III

When Pol III runs into the 5’ end of a downstream RNA primer,
it disassembles from the DNA template, and is replaced by Pol I
68
Details, continued:
Pol I digests away the RNA primer, and replaces it with DNA.
After Pol I has replaced all the RNA with DNA, it, in turn,
disassembles from the DNA template, and is replaced by DNA
ligase.
Pol III

Topoisomerase

Helicase
Pol I

Pol III
(Lagging strand of DNA) (Okazaki fragment)
(the beginning part
of what will become

Ligase joins the two DNA molecules.

the lagging strand
of DNA)

69
Here is another overview of the events at the two
replication forks in a replication “bubble”:

Helicase Leading strand

Lagging strand

70
All these events are occurring at an amazing speed;
the replication fork advances at a rate of
approximately 50 nucleotides per second.

50 nucleotides per sec.

71
 DNA polymerases are remarkably accurate; the wrong nucleotide is
incorporated only 1/100,000 nucleotides (10-5 error rate). But the
overall error rate is actually much less than 10-5, because Pol III
detects an incorrect nucleotide after it has incorporated it into the
growing chain. It stops, backs up, excises the mismatched base,
incorporates the correct base, and then continues on.
DNA polymerase makes a
mistake--adds a C instead of
This is called a T onto the end of the
growing DNA chain
“proofreading”
and the
excision of the
incorrect base
involves a 3’-5’ DNA polymerase backs up,
cuts out the C and then adds
exonuclease the correct T onto the end
of the growing DNA chain
activity of the
Pol III
enzyme.

Fig 14-14, 4th ed.

72
The proofreading activity of Pol III detects and repairs an
incorrectly added base about 99 times out of a hundred.
Proofreading therefore decreases the error rate of Pol
III from 10-5 to 10-7. But the actual observed overall
error frequency of DNA replication is even lower—another
one hundred fold lower: 10-9 ! This is because repair
enzymes run along behind the polymerase, scanning the
completed double helix for mismatch errors; eg, a G-T pair.
But how does the
repair machinery know
which base to excise
and replace- the G or
the T?

73
In bacteria, the repair enzymes can tell which is the new,
incorrect base (the G in this case), versus the correct,
template nucleotide (T in this case), because the adenine
nucleotides on the template strand are methylated at
regular intervals throughout its length.
The template strand is tagged
with methylated adenines

Takes time for the newly

synthesized strand to acquire
its methylated adenines

74
Here’s how it works:

Pol I uses its 5’-3’

exonuclease activity* to
remove the stretch of
nucleotides between the
two nicks, and then fills
in the gap.

* This is the same 5’-3’

exonuclease activity Pol I uses
to remove the primer RNA
during regular DNA synthesis
on the lagging strand.

75
The mechanism of
mismatched base
repair is an example
of a general class of
related repair
mechanisms called
“excision-repair”

76
Thus, the fidelity of DNA replication can be traced to
three distinct activities:
(1) Accurate selection of nucleotides to start with;
(2) immediate proofreading;
(3) postreplicative mismatch repair
Together, these processes result in an error rate of
approximately 10-9 for DNA replication.

But after DNA replication is complete, DNA can still be

damaged in any of a variety of ways: radiation damage,
hydrolysis, thermal damage, oxidative damage, etc. So
all cells have a large number of proteins devoted to
detecting and repairing other post-replicative damage.

77
For example, when skin cells are irradiated with UV light
(eg, during sunbathing), thymine dimers are formed:

Equivalent to Fig 4.17, 3rd Ed

Repair enzymes are constantly scanning the DNA,

and the thymine dimer is quickly detected. It is
then removed by excision repair.
78
 T-T photodimers
Here’s how
pyrimidine
dimers (such XP-C and 23B proteins
recognize and bind to T-T
as thymine photodimers, then recruit
proteins called TFIIH and RPA.
dimers) are
removed in
human cells:
The XP-G and XP-F
nucleases are recruited
(You don’t to make cuts on either
need to know side of the dimerized
these details pyrimidines.

for the test…)

Gap is filled in by
excision repair DNA
synthesis.

79
New Topic: Telomeres
Unlike bacteria (which have a circular chromosome), eukaryotic cells
have linear DNA molecules as their chromosomes. This leads to an
“end problem” in the replication of these molecules, due to the facts
that (a) DNA polymerase requires a primer, and (b) it only
synthesizes in a 5’ to 3’ direction. This “end problem” in the
replication of a linear DNA molecule leads to its shortening each
time it is replicated!
Here’s how the situation develops:

Pol III

This RNA primer can’t be replaced

with DNA! (See following slide.)

80
 In eukaryotic cells, either Pol I or a ribonuclease
called RNase H removes the RNA primer.

(Continued)

Pol III RNase H removes this RNA primer

Pol III falls off, Pol I digests away RNA &
replaces it with DNA; Ligase joins the strands.

After RNase H removes the RNA primer, an unreplicated 3’

overhang is left. Notice that the (red) daughter DNA 3’ – 5’
strand shown above is thereby shortened! The chromosome
continues to shorten with each round of DNA synthesis.
81
Animal cells, with their linear chromosomes, solve this
problem by attaching a long sequence of “junk” repetitive
DNA sequence (in humans: TTAGGG-TTAGGG- etc) at the
ends of their chromosomes. These long repetitive end
sequences are called the “telomeres”

So when the ends of the DNA molecule shorten with

each cycle of replication, only the “junk” telomeric
DNA is lost:

82
The enzyme that attaches this telomeric DNA is called
“telomerase”. It is an example of an unusual type of DNA
polymerase that uses an RNA molecule as its template
for the synthesis of DNA. Such polymerases are called
“reverse transcriptases”. In the case of telomerase, the
RNA template is part of the enzyme itself.
Here’s how it works:

Protein component

RNA template
component

Incoming
deoxyribonucleotide
83 triphosphates
After polymerizing the TTAGGG sequence onto the 3’
overhang end, the telomerase moves off to the right, and
adds another TTAGGG sequence, etc, etc.

Pol delta (= Pol III)

Then primase, DNA polymerase, and ligase will synthesize a

complementary strand to the added telomeric repeat sequences
in the usual way. (DNA polymerase δ does this work. Eukaryotic
Pol δ is equivalent to bacterial Pol III)
84
In stem cells and germline cells, telomerase is expressed, and
maintains the lengths of telomeres regardless of the number
of cell divisions:

But in all the rest of the body’s cells, expression of

telomerase is shut down late in embryological development.
This results in the shortening of the telomeres in most cells
during the lifetime of the animal (because each time a cell
divides [ie, the DNA replicates], the telomeres shorten).

85
In the kind of dysregulated growth that precedes the onset of
cancer, the telomeres are eventually lost altogether. This is detected
by the cell, and a signal is sent to arrest the growth of the cell. This
mechanism prevents many cancers; the successful cancer must find a
way to (1) shut off the “stop growth” signal sent from the naked end
of the DNA; and/or (2) turn on the expression of telomerase
Telomerase builds these long In normal somatic cells, telomerase is
telomeres in early embryo; then not expressed, so telomeres shorten
shuts off. each time DNA is replicated
Normal
growth

Excessive,
dysregulated
(This is an anti-
growth
cancer control.)
Signal for growth
arrest

“Successful” cancers (1) find a way

to shut off this signal; (2) turn on No telomeres!
expression of telomerase again.
86
 RNA Nucleotides
Composition ( 3 parts):
1- Ribose sugar (with O in 3rd carbon)
2- Phosphate group
3- One of 4 types of bases (all
containing nitrogen):
- Adenine
- Uracyl (only in RNA)
- Cytosine
- Guanine
 Ribonucleic Acid (RNA)
 RNA is much more abundant than DNA
 There are several important differences between RNA and DNA:
- the pentose sugar in RNA is ribose, in DNA it’s deoxyribose
- in RNA, uracil replaces the base thymine (U pairs with A)
- RNA is single stranded while DNA is double stranded
- RNA molecules are much smaller than DNA molecules
 There are three main types of RNA:
- ribosomal (rRNA), messenger (mRNA) and transfer (tRNA)
Types of RNA
Messenger RNA (mRNA)
 Its sequence is copied from genetic DNA
 It travels to ribsosomes, small granular
particles in the cytoplasm of a cell where
protein synthesis takes place

90 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
Ribosomal RNA (rRNA)
 Ribosomes are a complex of proteins and
rRNA
 The synthesis of proteins from amino
acids and ATP occurs in the ribosome
 The rRNA provides both structure and
catalysis

91 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
Transfer RNA (tRNA)
 Transports amino acids to the
ribosomes where they are joined
together to make proteins
 There is a specific tRNA for each
amino acid
 Recognition of the tRNA at the anti-
codon communicates which amino
acid is attached
92 Based on McMurry, Organic Chemistry,
Chapter 28, 6th edition, (c) 2003
 Transfer RNA
 Transfer RNA translates the genetic code from the messenger RNA
and brings specific amino acids to the ribosome for protein synthesis
 Each amino acid is recognized by one or more specific tRNA
 tRNA has a tertiary structure that is L-shaped
- one end attaches to the amino acid and the other binds to the mRNA
by a 3-base complimentary sequence
Ribosomal RNA and Messenger RNA
 Ribosomes are the sites of protein synthesis
- they consist of ribosomal DNA (65%) and proteins (35%)
- they have two subunits, a large one and a small one
 Messenger RNA carries the genetic code to the ribosomes
- they are strands of RNA that are complementary to the DNA
of the gene for the protein to be synthesized
 How DNA Works
1- DNA stores genetic information in
segments called genes
2- The DNA code is in Triplet Codons
(short sequences of 3 nucleotides
each)
3- Certain codons are translated by
the cell into certain Amino
acids.
4. Thus, the sequence of nucleotides in
DNA indicate a sequence of Amino
acids in a protein.
Transcription Process

 Several turns of the DNA double helix unwind, exposing

the bases of the two strands
 Ribonucleotides line up in the proper order by hydrogen
bonding to their complementary bases on DNA
 Bonds form in the 5  3 direction,

96 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
RNA—Ribonucleic Acid
• RNA is a messenger that allows the instruction
of DNA to be delivered to the rest of the cell
• RNA is different than DNA:
1.The sugar in RNA is ribose; the sugar in DNA
is deoxyribose
2.RNA is a single strand of nucleotides; DNA is
a double strand of nucleotides
3.RNA has Uracil (U) instead of Thymine (T)
which is in DNA
4.RNA is found inside and outside of the
nucleus; DNA is found only inside the
nucleus
Transcription of RNA from DNA
 Only one of the two DNA strands is transcribed into
mRNA
 The strand that contains the gene is the coding or
sense strand
 The strand that gets transcribed is the template or
antisense strand
 The RNA molecule produced during transcription is a
copy of the coding strand (with U in place of T)

98 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
Example of RNA Primary Structure
 In RNA, A, C, G, and U are linked by 3’-5’ ester bonds
between ribose and phosphate
The Parts of Transfer RNA
 There are 61 different tRNAs, one for each
of the 61 codons that specifies an amino
acid
 tRNA has 70-100 ribonucleotides and is
bonded to a specific amino acid by an ester
linkage through the 3 hydroxyl on ribose at
the 3 end of the tRNA
 Each tRNA has a segment called an
anticodon, a sequence of three
ribonucleotides complementary to the codon
sequence
100
 Protein Synthesis
 The two main processes involved in protein synthesis are
- the formation of mRNA from DNA (transcription)
- the conversion by tRNA to protein at the ribosome (translation)
 Transcription takes place in the nucleus, while translation takes
place in the cytoplasm
 Genetic information is transcribed to form mRNA much the same
way it is replicated during cell division
 RNA Polymerase
 During transcription, RNA polymerase moves along the DNA
template in the 3’-5’direction to synthesize the corresponding
mRNA
 The mRNA is released at the termination point
Processing of mRNA
 Genes in the DNA of eukaryotes contain exons that code
for proteins along with introns that do not
 Because the initial mRNA, called a pre-RNA, includes the
noncoding introns, it must be processed before it can be
read by the tRNA
 While the mRNA is still in the nucleus, the introns are
removed from the pre-RNA
 The exons that remain are joined to form the mRNA that
leaves the nucleus with the information for the synthesis of
protein
Removing Introns from mRNA
Transcription
 Several steps occur during transcription:
- a section of DNA containing the gene unwinds
- one strand of DNA is copied starting at the initiation point,
which has the sequence TATAAA
- an mRNA is synthesized using complementary base pairing
with uracil (U) replacing thymine (T)
- the newly formed mRNA moves out of the nucleus to
ribosomes in the cytoplasm and the DNA re-winds
The Structure of tRNA

109 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
Regulation of Transcription
 A specific mRNA is synthesized when the cell requires a
particular protein
 The synthesis is regulated at the transcription level:
- feedback control, where the end products speed up or slow
the synthesis of mRNA
- enzyme induction, where a high level of a reactant induces
the transcription process to provide the necessary enzymes for
that reactant
 Regulation of transcription in eukaryotes is complicated and
we will not study it here
The Ribonucleotides

112
 The Genetic Code
 The genetic code is found in the sequence of nucleotides in mRNA
that is translated from the DNA
 A codon is a triplet of bases along the mRNA that codes for a
particular amino acid
 Each of the 20 amino acids needed to build a protein has at least 2
codons
 There are also codons that signal the “start” and “end” of a
polypeptide chain
 The amino acid sequence of a protein can be determined by
reading the triplets in the DNA sequence that are complementary
to the codons of the mRNA, or directly from the mRNA sequence
 The entire DNA sequence of several organisms, including humans,
have been determined, however,
- only primary structure can be determined this way
- doesn’t give tertiary structure or protein function
Genetic code 1 19

The sequence of bases in DNA forms the

Genetic Code

A group of three bases (a triplet) controls

the production of a particular amino acid
in
the cytoplasm of the cell

The different amino acids and the order in

which they are joined up determines the sort
of protein being produced
Coding 21
For example

Cytosine

Adenine Codes for Valine

Thymine

Cytosine (C)
Guanine (G) Codes for Alanine
Adenine (A)
Triplet code 22

This is known as the triplet code

Each triplet codes for a specific amino acid

CGA - CAA - CCA - CCA - GCT - GGG - GAG - CCA -

Ala Val Gly Gly Arg Pro Leu Gly

The amino acids are joined together in the correct

sequence to make part of a protein

Ala Val Gly Gly Arg Pro Leu Gly

mRNA Codons and Associated Amino Acids
Reading the Genetic Code
 Suppose we want to determine the amino acids coded for in
the following section of a mRNA

5’—CCU —AGC—GGA—CUU—3’

 According to the genetic code, the amino acids for these

codons are:

CCU = Proline AGC = Serine

GGA = Glycine CUU = Leucine

 The mRNA section codes for the amino acid sequence of

Pro—Ser—Gly—Leu
 Translation and tRNA Activation

 Once the DNA has been

transcribed to mRNA, the
codons must be tranlated to the
amino acid sequence of the
protein
 The first step in translation is
activation of the tRNA
 Each tRNA has a triplet called
an anticodon that complements
a codon on mRNA
 A synthetase uses ATP
hydrolysis to attach an amino
acid to a specific tRNA
 Initiation and Translocation
 Initiation of protein synthesis occurs when a mRNA attaches to
a ribosome
 On the mRNA, the start codon (AUG) binds to a tRNA with
methionine
 The second codon attaches to a tRNA with the next amino acid
 A peptide bond forms between the adjacent amino acids at the
first and second codons
 The first tRNA detaches from the ribosome and the ribosome
shifts to the adjacent codon on the mRNA (this process is called
translocation)
 A third codon can now attach where the second one was before
translocation
Termination
 After a polypeptide with all the amino acids for a protein is
synthesized, the ribosome reaches the the “stop” codon:
UGA, UAA, or UAG
 There is no tRNA with an anticodon for the “stop” codons
 Therefore, protein synthesis ends (termination)
 The polypeptide is released from the ribosome and the
protein can take on it’s 3-D structure
(some proteins begin folding while still being synthesized,
while others do not fold up until after being released from
the ribosome)
DNA and enzymes 23

The proteins build the cell structures

They also make enzymes

The DNA controls which enzymes are made and
the enzymes determine what reactions take place

The structures and reactions in the cell determine

what sort of a cell it is and what its function is

So DNA exerts its control through the enzymes

Genes 24

A sequence of triplets in the DNA molecule may

code for a complete protein

Such a sequence forms a gene

There may be a thousand or more bases in

one gene
Conformation around N-Glycosidic Bond

 Relatively free rotation can occur around the N-glycosidic

bond in free nucleotides
 The torsion angle about the N-glycosidic bond (N-C1') is
denoted by the symbol c
 The sequence of atoms chosen to define this angle is O4'-
C1'-N9-C4 for purine,
and O4'-C1'-N1-C2 for pyrimidine derivatives
 Angle near 0corresponds to syn conformation
 Angle near 180 corresponds to anti conformation
 Anti conformation is found in normal B-DNA
 Replication of Genetic Code
• Strand separation occurs first
• Each strand serves as a template
for the synthesis of a new strand
• Synthesis is catalyzed by enzymes
known as DNA polymerases
• Newly made DNA molecule has one
daughter strand and one parent strand.
“It has not escaped our notice that the specific pairing
we have postulated immediately suggests a possible
copying mechanism for the genetic material”

Watson and Crick, in their Nature paper,1953

Messenger RNA:
Code Carrier for the Sequence of Proteins
• Is synthesized using DNA template
• Contains ribose instead of deoxyribose
• Contains uracil instead of thymine
• One mRNA may code for more than
one protein
 Factors Affecting DNA Denaturation
 The midpoint of melting (Tm) depends on base
composition
 high CG increases Tm

 Tm depends on DNA length

 Longer DNA has higher Tm
 Important for short DNA

 Tm depends on pH and ionic strength

 High salt increases Tm