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Nucleic Acids
DNA & RNA
Lecture 8 (Finals)

What do they do ?
Dictate amino-acid sequence
in proteins
Give information to
chromosomes, which is then
passed from parent to
offspring

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What are they ?

The 4th type of

macromolecules
The chemical link between
generations
The source of genetic
information in chromosomes

Definitions
Nucleic acids are polymers of nucleotides
A complex organic substance present in living cell, whose molecule consist of many
nucleotide (Building block of nucleic acid) linked in a long chain having varietyof
roles in cellular metabolism.
Nucleic acids largest and heaviest biomolecules, Molecular weight 30,000-millions

Nucleotides are carbon ring structures containing nitrogen linked to a

5-carbon sugar (a ribose)
5-carbon sugar is either a ribose or a deoxy-ribose making the
nucleotide either a ribonucleotide or a deoxyribonucleotide
In eukaryotic cells nucleic acids are either:
Deoxyribose nucleic acids (DNA)
Ribose nucleic acids (RNA)
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (tRNA)

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Functions of Nucleic Acids

 Nucleic Acid Functions:

 Storage of genetic info (DNA)
 Transmission of genetic info (mRNA)
 Processing of genetic information (ribozymes)
 Protein synthesis (tRNA and rRNA)

RNA
Involved in the transcription/translation of genetic material (DNA)

Genetic material of some viruses

DNA fingerprinting is a method used by forensic

experts to determine paternity.
It is also used for the identification of criminals.
It has also played a major role in studies regarding
biological evolution and genetics.
Required for storage and expression of genetic
information.
They are the energy currency in metabolic
transactions (nucleotides).

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DNA
DNA – Deoxyribonucleic Acid
•DNA controls all living processes including
production of new cells – cell division
•DNA carries the genetic code – stores and
transmits genetic information from one
generation to the next
•Chromosomes are made of DNA
•DNA is located in the nucleus of the cell

Nucleotide Structure
Despite the complexity and diversity of life the structure of DNA is
dependent on only 4 different nucleotides

Diversity is dependent on the nucleotide sequence

All nucleotides are 2 ring structures composed of:

5-carbon sugar : -D-ribose (RNA)
-D-deoxyribose (DNA)

Base Purine
Pyrimidine

Phosphate group A nucleotide WITHOUT a phosphate group is a

NUCLEOSIDE

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Two types of Nucleotides

(depending on the sugar they contain)
1- Ribonucleic acids (RNA)
The pentose sugar is Ribose (has a
hydroxyl group in the 2rd carbon---
OH)
2- Deoxyribonucleic acids (DNA)
The pentose sugar is Deoxyribose
(has just a hydrogen in the same
place--- H) Deoxy = “minus oxygen”

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Pentose Sugars
 The sugars have their carbon atoms numbered with primes
to distinguish them from the nitrogen bases

Ribose sugar-
presence of OH at
position 2

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Purine and Pyrimidine

 Pyrimidine contains two pyridine-like nitrogens in a six-
membered aromatic ring
 Purine has 4 N’s in a fused-ring structure. Three are basic
like pyridine-like and one is like that in pyrrole

12 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003

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Nitrogenous Base-Purines
 Purines – Contains Adenine (A) and Guanine (G) nitrogen bases
 Heterocyclic aromatic compound
 Pyrimidines ring fused with imidazole ring
 Carbon atoms in purine ring are numbered in anti-clockwise
direction
 But in imidazole ring numbered in clockwise direction.
 C-4 and C-5 common to both rings
 Four nitrogen atoms present at 1st, 3rd, 7th, and 9th position.

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Nitrogenous Base-- Pyrimidines

 Pyrimidines (C4H4N2) – contains Thymine (T),
Cytosine (C) and Uracil (U) nitrogen bases
 Single Aromatic Compound, having six membered
heterocyclic ring system.
 2 nitrogen atoms at 1st and 3rd position
 4 carbon atoms at 2nd, 4th, 5th and 6th position
 In Pyrimidines C-2 is linked to oxygen by double bond.

DNA and RNA Only in RNA DNA and Traces in

tRNA

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Names of Nucleosides and Nucleotides

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Nucleosides and Nucleotides

 A nucleoside consists of a nitrogen base linked by a glycosidic
bond to C1’ of a ribose or deoxyribose
 Nucleosides are named by changing the the nitrogen base
ending to -osine for purines and –idine for pyrimidines

 A nucleotide is a nucleoside that forms a phosphate ester with

the C5’ OH group of ribose or deoxyribose
 Nucleotides are named using the name of the nucleoside
followed by 5’-monophosphate

Nucleotide
Nucleoside Sugar + Nitrogenous base +
Sugar + Nitrogenous base Phosphate group

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AMP, ADP and ATP

 Additional phosphate groups can be added to the nucleoside 5’-
monophosphates to form diphosphates and triphosphates
 ATP is the major energy source for cellular activity

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Nucleotide Function

Building blocks for DNA and RNA

Intracellular source of energy - Adenosine triphosphate (ATP)
Second messengers - Involved in intracellular signaling
(e.g. cyclic adenosine monophosphate [cAMP])
Intracellular signaling switches (e.g. G-proteins)
Signal transduction (cAMP)

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How the nucleotides are linked together !!

Phosphodiester bond: (3’-5’)
 The nucleotide of DNA and RNA are linked together by phosphate
“bridges”.
 The 5-phosphate group of one nucleotide unit is linked to the 3-hydroxyl
group of the next nucleotide, creating a phosphodiester linkage/bond.

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How the nucleotides are linked together !!

Phosphodiester bond:
The backbone of both RNA and DNA are hydrophilic. The phosphate group gives negative charge.

5’ 3’

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Sanger dideoxy sequencing incorporates dideoxy

nucleotides, preventing further synthesis of the DNA
strand

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Formation of Polynucleotides:
Polynucleotide chains do not form through dehydration,
since this reaction is thermodynamically unfavored.

The metastability of DNA and RNA allow for controlled

-H2O turnover and reorganization via base catalysis (e.g.
Go’=25 kJ/mol nucleases). More to come on this…
+H2O
cat. -OH
2 Go’PPio-PO4=-19 kJ/mol

Metastable

How do polynucleotides form? Coupled reactions!

Breaking high energy phosphate bonds (NTP
to NMP+PPi, and PPi to orthophosphate)
provides a favorable thermodynamic driving
force to yield polynucleotides Go’NTPNMP=-31 kJ/mol

NTP + H2O NMP + PPi Go’=-31 kJ/mol

DNAN+NMP DNA(N+1)+H2O Go’=25 kJ/mol
PPi + H2O 2 HPO42- Go’=-19 kJ/mol
Go’Polynucleotide=25 kJ/mol
DNAN+NTP DNA(N+1)+2HPO42- Go’=-25
kJ/mol

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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

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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

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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

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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

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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
 The complementary base pairs are A-T and
G-C
 Each pair consists of a purine and a pyrimidine, so
they are the same width, keeping the two strands
at equal distances.

A T (2 H-bonds)

G C (3 H-bonds)

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Nucleic Acid Structure

“Base Pairing”
5’ 3’

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

3’ 5’
DNA base-pairing is antiparallel

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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

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Nucleic Acid Structure

Polymerization

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

P
+ P P
N

C
(PPi)
S
P P P
N
C
S

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Generalized Structure of DNA

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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’

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Example of DNA Primary Structure

 In DNA, A, C, G, and T are linked by 3’-5’ ester bonds
between deoxyribose and phosphate

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Nucleic Acid Structure

Polymerization

Nucleotide
Sugar Phosphate
“backbone”

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Describing a Sequence
 Chain is described from 5
ends, 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

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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

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Chargaff’s base equivalence rule

 Purines = Pyrimidines,
 [A+G] = [T+C], [A+G]/[T+C]=1
 Molar concentration of Adenine is always equal to thymine, Similarly, molar conc. of
guanine is equal to cytosine
 Sugar and phosphate occur in equimolar proportions
 A-T base pairs are rarely equal to C-G base pairs
 The ratio of [A+T]/[G+C] is variable but constant for a species. It can used to identify
the source of DNA. The ratio is low in primitive organisms and higher in advanced
ones.

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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.
 Most energy-favorable conformation for double-
stranded DNA to form
 Shape and size are uniform for all life (i.e. DNA is
identical)
 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. Without anti-parallel base pairing
this conformation could not exist

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Structure of DNA

why do these base pairs arise within a duplex DNA!!!

 The specificity of Watson-Crick base pairing results from both the hydrogen-
bonding factors we described, and steric restrictions imposed by the two
deoxyribose–phosphate backbones.
 If we consider the steric restrictions first, we can start by asking how much ‘room’
there is between the two backbones and which bases will fit within this space to
make suitable pairs.

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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

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• 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
C always pairs with G in DNA
The paired strands are coiled into a spiral
called
Nucleotide A DOUBLE HELIX
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Nucleic Acid Structure

The double helix
Major grooves are
critical for binding
proteins that
regulate DNA
function
Minor
Groove

Major
Groove

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Watson and Crick model

• Is their any worth of these major and minor grooves !!

 As a consequence (of these grooves), the atoms on the edges of each

base

within these grooves are accessible from outside the helix, forming two

types of binding surfaces.

 DNA-binding proteins can “read” the sequence of bases in duplex DNA by

contacting atoms in either the major or the minor grooves.

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Why did DNA, rather than RNA, evolve to be the carrier of genetic information
in cells?
 The hydrogen at the 2′ position in the deoxyribose of DNA makes it a far more stable
molecule than RNA, which instead has a hydroxyl group at the 2′ position of ribose
 The 2′-hydroxyl groups in RNA participate in the slow, OH− catalyzed hydrolysis of
phosphodiester bonds at neutral pH

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Hydrophobic
Structure of DNA
Why the DNA is twisted !!
Hydrophilic

 DNA is coiled into chromosomes and tightly packed in the

nucleus of our cells.
 The twisting of DNA results from both hydrophilic and
hydrophobic interactions between DNA molecules and
water in a cell.
 The nitrogenous bases are hydrophobic, Since the cell
cytoplasm and cytosol contain water-based liquids, the
nitrogenous bases want to avoid contact with cell fluids.
 DNA is arranged such that the phosphate and the sugar
backbone are on the outside and in contact with fluid, while
the nitrogenous bases are in the inner portion of the
molecule.
 To further prevent contact with cell fluid, the molecule twists
to reduce the space between the nitrogenous bases and the
phosphate and sugar strands.

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Factors Affecting DNA Denaturation

DNA strand separation
DNA double helix can be disrupted/separated because of
1. Change in PH
2. Change in Temperature
What is melting temperature?
The temperature at which one-half of the helical structure is
lost is defined as melting temperature.
What is Denaturation?
The complete loss of helical structure in DNA is called
Denaturation.

 The midpoint of melting (Tm) depends on

the base composition
 high CG increases Tm  Tm depends on pH and ionic
 Tm depends on DNA length strength
 Longer DNA has higher Tm  High salt increases Tm
 Important for short DNA

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Different forms of DNA

There are six known different morphological forms of DNA double helix. These have been
named as A, B, C, D, E, and Z DNA.
Out of these six forms, only B-DNA and Z-DNA are found to occur as cellular DNA.
In the number of base pairs present per turn in them
angle between the base pairs
Diameter of DNA molecule
The hardness of coiling of the double helix

(1) A-DNA (2) B-DNA

• Discovered by Rosalind Franklin • Named by Rosalind Franklin
• Right-Handed helix • Majority of the DNA in a cell is in B-DNA
• Form by the dehydration of B- conformation.
DNA. • Right-Handed helix
• Bp per helix= 11bp • Bp per helix = 10-10.4
• Major Grooves= Narrow and deep • Major grooves = wide and deep
• Minor Grooves = wide and deep • Minor Grooves = Narrow and deep

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(3) Z-DNA (4) C-DNA, 5) D-DNA and E-DNA

• Discovered by Andres Wang and They do not occur under normal / natural condition.
Alexander Rich.
• Left-handed helix.
• It is one of the biologically active forms
of DNA found in vivo in the cells.
• The exact biological function of Z-DNA
is not clear.
• Bp per helix = 12bp
• Major Grooves = flat major Grooves
• Minor Grooves = Narrow and deep

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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 indicates a sequence of Amino
acids in a protein.

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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)

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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

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Types of RNA

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Messenger RNA (mRNA)

 Its sequence is copied from genetic DNA
 It travels to ribosomes, small granular
particles in the cytoplasm of a cell where
protein synthesis takes place

59 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003

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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

60 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003

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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
61 Based on McMurry, Organic Chemistry,
Chapter 28, 6th edition, (c) 2003

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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

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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
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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

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Nucleic Acids and Heredity

 Processes in the transfer of genetic information:
 Replication: identical copies of DNA are made
 Transcription: genetic messages are read and carried out
of the cell nucleus to the ribosomes, where protein
synthesis occurs.
 Translation: genetic messages are decoded to make
proteins.

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The central dogma of

molecular biology

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DNA Replication  The process by which a double-stranded DNA

molecule is copied to produce two identical DNA molecules

• 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

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Replication
DNA replication involves several processes:
- first, the DNA must be unwound, separating
the two strands
- the single strands then act as templates for
the synthesis of the new strands, which are
complementary 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’s DNA comes from the parent DNA
and one strand is new
The energy for the synthesis comes from the
hydrolysis of phosphate groups as the
phosphodiester bonds form between the bases

So that when the cell divides, each nucleus contains identical

DNA

This process is called replication

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STEP 1: Initiation
• Hydrogen bonds between base
pairs are broken by the enzyme
Helicase and the DNA molecule
unzips
• DNA molecule separates into
complementary halves.
• Two chains run
antiparallel.
• Two chains differ in sequence
• (the sequence is read
from 5’ to 3’)

Figure 5-14 Schematic representation of

the strand separation in duplex DNA
resulting from its heat denaturation.

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STEP 2: Elongation
Nucleotides match up with complementary bases

Free nucleotides abundant in nucleus

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

New Strand
Original Strand
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• Mutations occur when

copying errors cause a
change in the sequence of
DNA nucleotide bases.

• DNA polymerase adds 50

nucleotides/second.
• DNA polymerase can proofread
its own work and does excision
repair
• 1 in 10,000 bases are in error.
• After proofreading, rate of
mutation is 1 in 10,000,000

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Diagram Examples of DNA Replication:

(You could see DNA replication represented different ways.)

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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

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TRANSCRIPTION
 Transcription is the process by which the information in a
strand of DNA is copied into a new molecule of
messenger RNA (mRNA).
 Transcription is carried out by an enzyme called RNA
polymerase and a number of accessory proteins called
transcription factors.
 Transcription occurs in the three steps—
 1. Initiation
 2. Elongation
 3. Termination

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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,

76 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003

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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)
 The newly formed mRNA moves out of the nucleus
to ribosomes in the cytoplasm and the DNA re-
winds

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Steps of Transcription
1. Initiation: An enzyme RNA polymerase binds to the promoter region.
One strand of DNA is copied starting at the initiation point, which has the
sequence TATA box (promoter region)
• Unwind the double-helix and form a transcription bubble.
• RNA polymerase reads the nucleotide sequence and copy to m-RNA.

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1. Elongation: RNA-polymerase moves along the template strand and

synthesizes an m-RNA molecule.
 Elongation RNA Polymerase moves in the 5’ to 3’ direction and is
complimentary to the DNA template Works at up to 60 nucleotides/second
2. Termination: Termination RNA Polymerase reaches the terminator
region of the protein-encoding gene All the enzymes and factors are
released The product of these 3 steps is called immature or pre-
mRNA. There are two ways of termination-
• i. Rho-dependent: A protein factor called Rho-factor is responsible for
disrupting RNA- polymerase from the template strand.
• ii. Rho-independent: A loop forms at the end of the RNA molecule to detach
itself.

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RNA Processing
• Most eukaryotic protein-encoding genes contain non-coding
segments called introns, which break up the amino acid coding
sequence into segments called exons RNA Processing includes
modification and splicing
• RNA Processing Modification: At the 5' end, a cap consisting of
a modified GTP (guanosine triphosphate) is added. This occurs
at the beginning of transcription. The 5' cap is used as a
recognition signal for ribosomes to bind to the mRNA
• At the 3' end, a poly(A) tail of 150 or more adenine nucleotides
is added. The tail plays a role in the stability of the mRNA.

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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 the tRNA can
read it
 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

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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

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Translation: Protein Synthesis

 The language of nucleic acids is translated into the language of proteins
Nucleic acids have a 4-letter language Proteins have a 20-letter language.
 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

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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
 The Genetic Code If 3 RNA bases code for 1 amino acid, RNA could code for
4X4X4 = 64 amino acids. More than enough coding capacity for 20 amino acids
 Code is redundant for most amino acids: Each of the 20 amino acids needed to
build a protein has at least 2 codons
 Some codons 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, has been
determined, however,
- only primary structure can be determined this way
- doesn’t give tertiary structure or protein function

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Coding

For example:

Cytosine

Adenine Codes for Valine

Thymine

Cytosine (C)
Guanine (G) Codes for Alanine
Adenine (A)

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Triplet code

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

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mRNA Codons and Associated Amino Acids

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Key components of Translation process:

mRNA

Ribosome

tRNA

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Translation and tRNA Activation

 Once the DNA has been

transcribed to mRNA, the
codons must be translated to the
amino acid sequence of the
protein
 The first step in translation is
the 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

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Steps of Translation:
• 1. INITIATION: The ribosome assembles around the target
mRNA. The first tRNA is attached at the start codon.

• 2. ELONGATION: The t-RNA forms an amino acid by read

the codon sequence. The ribosome then moves to the
next m-RNA codon to continue the process and creating
an amino acid chain.

• 3. TERMINATION: When a peptidyl t-RNA binds with a

stop codon, then the ribosome folds the polypeptide into
its final structure.

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Initiation and Translocation

 Initiation of protein synthesis occurs when a mRNA attaches to a
ribosome. 5’ G-cap of mRNA binds to ribosome Start codon AUG.
 On the mRNA, the start codon (AUG) binds to a tRNA with
methionine at P-site
 The second codon attaches to a tRNA with the next amino acid at A-
site.
 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

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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)

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Translation, Polypeptides, and Mutations

• Normally, the genetic code is translated, and the correct protein is formed from a
long chain of amino acids. Translation of codons is dependent on the reading
frame , or a grouping of codons in a gene transcript e.g. AAU GCG GAC UAC GGC
AAC GCC
• Mutations: Any change in the nucleotide sequence of DNA.
• Mutations can involve large sections of chromosomes or single base pairs
Mutations can change the reading frame of a gene
transcript.
• Changes in one or a few bases is called a Point Mutation 2 Types: Substitution or
Insertion/Deletions

Sickle Cell Anemia:

Normal Hemoglobin Sickle Cell Hemoglobin
DNA: GGA CTT GCA DNA: GGA CAT GCA
mRNA: CCU GAA CGU mRNA: CCU GUA CGU
A.A.: PRO GLU ARG A.A.: PRO VAL ARG

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• Deletion or insertion mutations are most disruptive because they

change the reading frame, causing a frame shift Substitution
mutations have varied impact on amino acid sequences.
• Substitutions of 1st or 2nd base in codon almost always changes the
amino acid Substitution of 3rd base in codon does not always
change the amino acid
• What causes mutations?
• Errors in DNA Replication
• Errors in chromosome crossover in meiosis
• Mutagens are physical or chemical factors that cause mutations UV
Radiation and X-Rays Chemicals like DDT
• Many mutations are harmful and cause the organism to die or
function incorrectly.
• Some mutations are beneficial and help the organism to survive.
(Peppered Moths) If mutations are present in gametes , they can be
passed on to offspring. This is the driving force of Natural Selection.

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