2. Nucleic acids
Nucleic acids are molecules that store information for cellular
growth and reproduction
Are polymers of nucleotides
Contain carbon, hydrogen, oxygen, nitrogen and phosphorus
There are two kinds of Nucleic acids
1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)
2
3. Both types of nucleic acids are present in all plants and animals
Virus has either RNA or DNA, but not both
DNA is found mainly in the nucleus
Extra nuclear DNA also exists in mitochondria and
chloroplasts
Most of the RNA (90%) is present in the cell cytoplasm and
a little (10%) in the nucleolus
3
… Cont’d
4. 4
A Nucleotide consists of three components
1. Nitrogenous Bases (Purine & Pyrimidine)
2. Pentose sugar (Ribose/Deoxy ribose)
3. Phosphoric Acid (H3PO4)
5. There are two types of nitrogenous bases
1. Purine
• heterocyclic aromatic organic compound that consists of a
pyrimidine ring fused to an imidazole ring
• Adenine and guanine are the two purines which found in both
RNA and DNA
5
6. 6
II. Pyrimidine
• A single-ringed, crystalline organic base, C4H4N2
1. Uracil found in RNA molecules only
2. Thymine found in DNA molecules only
3. Cytosine found in both RNA and DNA
7. Pentose Sugar
• There are two related pentose sugars:
- RNA contains ribose
- DNA contains deoxyribose
• The sugars have their carbon atoms numbered with primes to
distinguish them from the nitrogen bases
7
8. Nucleosides and Nucleotides
Nucleosides
are glycosylamines or nucleotides without a phosphate group
consists of N base linked by a β- glycosidic bond to C1’ of a ribose or
deoxyribose
named by changing the nitrogen base ending to
- osine for purines and
– idine for pyrimidines
Nucleosides containing ribose are called ribonucleosides,
Nucleosides containing deoxyribose are called deoxyribonucleosides
8
9. Nucleotides
Nucleotides are the phosphoric acid esters of nucleosides
The phosphate is always esterified with the sugar moiety
OH groups of pentoses, especially at C3 and C5, are involved
forming 3′, 5′- phosphodiester bond between adjacent pentose
residues
Nucleotides are named using the name of the nucleoside followed
by 5’-monophosphate
The prefix 'd' is used to indicate if the sugar is deoxyribose e.g.
dAMP
9
10. The term mononucleotide is used when a single phosphate moiety is added to a
nucleoside
Thus adenosine monophosphate (AMP) contains: adenine + ribose + phosphate
Addition of 2nd or 3rd phosphates to the nucleotide results in nucleoside
diphosphate (ADP) or triphosphate (ATP), respectively
10
12. 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
12
13. ATP
ATP is the universal energy currency
formed during oxidative processes by trapping the released energy
in the high energy phosphate bond
13
14. Functions of
Nucleotides
As carriers of chemical energy- ATP : a source of chemical energy
to drive many biochemical reactions
As components of enzyme cofactors- Many enzyme cofactors and
coenzymes (coenzyme A, NAD+ and FAD) contain adenosine as
part of their structure
Nucleic acid synthesis
Protein synthesis
14
15. DNA
Polymer of deoxy ribonucleotides
Consists of deoxyriboses linked by phosphodiester bridges
Nucleotides are covalently linked together to form a strand of DNA
The position of the internucleotide linkage is between C3′ and C5′
DNA is a right handed double helix
The double helical structure of DNA was proposed by Watson and
Crick in 1953
15
16. Consists of two polydeoxyribonucleotide chains (strands) twisted
around each other on a common axis
The two strands are antiparallel, not identical but complementary
to each other due to base pairing
Each turn of the helix is with 10 pairs of nucleotides
The two strands are held together by H- bonds formed by
complementary base pairs
16
… Cont’d
17. The A-T pair has 2 H- bonds while G-C pair has 3 H- bonds
The G = C is 50% stronger than A=T
The hydrogen bonds are formed between a purine & pyrimidine
only (A-T, T-A, G-C and C-G)
17
… Cont’d
18. Primary Structure of Nucleic Acids
primary structure of a nucleic acid is the nucleotide sequence
nucleotides in nucleic acids are joined by phosphodiester bonds
The 3’-OH group of the sugar in one nucleotide forms ester bond
to the phosphate group on the 5’-carbon of the sugar of the next
nucleotide
18
20. Reading Primary Structure
A nucleic acid polymer has a free 5’-P 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’
Where all the phosphodiester bonds are
5‘3'
20
21. Example of RNA Primary
Structure
In RNA, A, C, G, and U are linked by 3’-5’ ester bonds
between ribose and phosphate
21
22. Example of DNA Primary Structure
In DNA, A, C, G, and T are linked by 3’-5’ ester bonds between
deoxyribose and phosphate
22
23. Secondary Structure: DNA Double Helix
In DNA, two strands of nucleotides wind together in a double helix
- the strands run in opposite directions
- the bases 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
23
24. 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
24
… Cont’d
26. flow of information in the cell starts at DNA, which replicates to
form more DNA
Information is then ‘transcribed” into RNA, and then “translated”
into protein
The proteins do most of the work in the cell
Information does not flow in the other direction
This is a molecular version of the incorrectness of “inheritance of
acquired characteristics”
Changes in proteins do not affect the DNA in a systematic manner
(although they can cause random changes in DNA)
26
Central Dogma of Molecular Biology
29. DNA REPLICATION
Synthesis of DNA is called replication
DNA replication starts at the early stage of cell division.
It is the way in which the genetic information can pass from parental cell to daughter
cell
The double helical structure of DNA depends on the base complementarity
complementarity represents the fundamental basis for the formation of new DNA
strands from the parent DNA strand in a semi conservative manner
In this process, two daughter DNA’s are produced, each has one parent strand
(conserved) and newly synthesized strand
DNA replication, the basis for biological inheritance, is a fundamental process
occurring in all living organisms to copy their DNA.
In the process of "replication" each strand of the original double-stranded DNA
molecule serves as template for the reproduction of the complementary strand.
Two identical DNA molecules have been produced from a single double-stranded
DNA molecule.
30. DNA replication
The basic rules of replication of Nucleic acid
Nucleotide monomers are added one by one to the growing strand by DNA polymerase
The synthesized strand is complementary to the parent strand
Enzymes in Replication
Enzymes unwind the two strands
DNA polymerase attaches complementary nucleotides
DNA ligase fills in gaps
Enzymes wind two strands together
32. Steps of DNA Replication
Origin of DNA - Replication starts at particular DNA sequence called origin.
To start DNA replication origin is recognized by DNA Gyrase is a protein
which recognizes DNA origin. The main function of gyrase is to put the
negative super twist on double helix of DNA.
But the two strands of DNA can be separated by special protein
Helicase.
Helicase melts the hydrogen bond of the two strands of DNA
To prevent the recoiling back to the double helix, single strand binding
protein (SSB) plays the role.
SSB binds to the single stranded DNA and thus protects the single
strand from rejoining.
34. Steps of Replication…
Primer synthesis: After the two strands of DNA are separated at origin, short
complementary RNA to the single strand parental DNA is synthesized. This RNA is
called a primer
The primer is synthesized by the enzyme called primase.
The primer grows in the 5’ → 3’ direction which is anti-parallel to the parental DNA.
Primer is needed to provide 3’- OH group for building of new DNA by DNA polymerase.
Nascent DNA Synthesis:-
After the primer is synthesized the primase become inactive.
There is step by step addition of Deoxyriboncleotide at 3’ – OH end of the primer
continues. The enzyme is called DNA polymerase
Nascent DNA grows in the 5’→ 3’ direction which is anti-parallel to the template strand.
The nascent synthesis of DNA takes place at both strands of the template or parental
DNA.
35. DNA Replication
new
new old old
• Each parent strand
remains intact
• Every DNA molecule
is half “old” and half
“new”
“semi-conservative”
replication
36. 1. Enzymes unwind
the parental double
helix.
Parental
strand
4.The lagging strand is synthesized discontinuously.
RNA polymerase synthesizes a short RNA primer,
which is then extended by DNA polymerase
DNA
polymerase
---RNA primer
RNA
polymera
se
DNA
polymerase
Okazaki
fragment
DNA
ligase
5. DNA ligase joins the discontinuous
fragments of the lagging strand.
2.Proteins Stabilize the
unwound parental DNA
DNA
polyme
rase
3. The leading strand is
synthesized continuously
by DNA polymerase
A summary of events at the DNA replication fork.
37. Important Enzymes in DNA Replication, Expression, and Repair
DNA Gyrase Relaxes supercoiling ahead of the replication fork
Helicase Unwinds double-stranded DNA
Primase Makes RNA primers from a DNA template
DNA Polymerase Synthesizes DNA: proofreads and repairs DNA
DNA Ligase Makes covalent bonds to join DNA strands: joins
Okazaki fragments and new segments in excision
repair
RNA Polymerase Copies RNA from a DNA template
38. RNA
RNA is a polymer of ribonucleotides held together by
3',5'- phosphodiester bridges
RNA has certain similarity with DNA structure
Both have adenine, guanine and cytosine. Both have
nucleotides linked by phosphodiester bond, in 5’-3’direction.
Both have important role in protein synthesis.
RNA and DNA also have specific differences
38
39. Differences between RNA and DNA
DNA RNA
Pyrimidine Thymine Uracil
Sugar Deoxyribose Ribose
Site Nucleus, mitochondria
but never in cytosol
Nucleus, ribosome, Nucleolus,
cytosol, mitochondria
Strands Two helical strands Single strand
Carries genetic
information
They Carries genetic
information
Only m-RNA carries genetic
information
DNA can
synthesize RNA by
transcription
yes Usually RNA can’t form DNA,
except by reverse transcriptase. 39
41. There are 3 major types of RNA
1. Messenger RNA (mRNA) : 5-10%
2. Transfer RNA (tRNA) : 10-20%
3. Ribosomal RNA (rRNA) : 50-80%
41
42. 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
Transfer genetic information from genes to ribosomes to
synthesise protein
42
43. Ribosomal RNA
is the catalytic component of the ribosomes.
rRNA molecules are synthesized in the nucleolus.
In the cytoplasm, ribosomal RNA and protein combine to form a
nucleoprotein called a ribosome.
Ribosomes are the sites of protein synthesis
- they consist of ribosomal RNA (65%) and proteins (35%)
- they have two subunits, a large one and a small one
43
44. 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
44
45. Structural characteristics of t- RNA
Secondary structure
(Clover leaf structure)
All t-RNA contain 4
main arms or loops
a) Acceptor arm(Amino
acid arm)
b) Anticodon arm
c) D HU arm
d) TΨ C arm
45
Dihydrouridine (D),
Ribothymidine (T) &
Pseudouridine ()
46. RNA Synthesis
Transcription is the DNA-directed synthesis of RNA
Transcription is the synthesis of complementary strand of RNA from a DNA template.
Messenger RNA is transcribed from the template strand of a gene.
RNA polymerase separates the DNA strands at the appropriate point and bonds the RNA
nucleotides as they base-pair along the DNA template.
Like DNA polymerases, RNA polymerases can add nucleotides only to the 3’ end of the
growing polymer.
Genes are read 3’->5’, creating a 5’->3’ RNA molecule
RNA polymerase does not need a primer to initiate transcription.
The RNA product does not remain base-paired to the template DNA strand.
Transcription occurs in three phases:-
1. Initiation 2. Elongation 3. Termination
47. Initiation
Initiation: A promoter is the DNA sequence that initially binds the RNA polymerase.
Transcription factors recognize the promotor region and bind to the promoter.
After they have bound to the promotor, RNA polymerase binds to transcription factors
to create a transcription initiation complex.
RNA polymerase then starts transcription.
Only one of the DNA strands acts as a template
47
48. Elongation & Termination
Elongation: Once the RNA polymerase has synthesized a short stretch
of RNA approximately ten bases, it shifts into the elongation phase.
As RNA polymerase moves along the DNA, it untwists the double
helix, 10 to 20 bases at time.
The enzyme adds nucleotides to the 3’ end of the
growing strand.
Behind the point of RNA synthesis, the double helix
re-forms and the RNA molecule peels away
Termination: Once the polymerase has transcribed the length of the
gene, it must stop and release the RNA product.
48
51. Protein synthesis (Translation)
Proteins (also known as polypeptides) are made of amino acids arranged in a linear chain and folded into a
globular form.
Translation:- is the process of decoding the mRNA into a polypeptide chain
Ribosomes read mRNA three bases or 1 codon at a time and construct the proteins
Under translation the base sequence of mRNA determines the amino acid sequences in protein
The components required for translation include:
A. mRNA,
B. ribosomes,
C. tRNA,
D. Genetic code
E. aminoacyl tRNA synthetases,
51
53. Translation…..
A. mRNA (Messenger RNA)
Messenger RNA consists of leader, reading frame, and trailer sequences.
Sequences of mRNAs vary because amino acid coding sequences (reading frames)
differ, and because leader and trailer sequences differ
55. Translation…..
B.Ribosomes
Ribosomes, the organelles on which the mRNA is translated, consist of
two subunits, each of which contains rRNA and ribosomal proteins.
The ribosome has three binding sites for tRNA
◦ The P site
◦ The A site
◦ The E site
56. Translation…..
C. tRNAs
tRNAs bring amino acids to the ribosome during translation to
be assembled into polypeptide chains.
D. The Genetic Code
Genetic information is encoded as a sequence of
nonoverlapping base triplets, or codons
The gene determines the sequence of bases along
the length of an mRNA molecule
57. The Genetic Code
Codons: 3 base code for the production of a specific amino acid, sequence of three of the four
different nucleotides
Each codon signifies start, stop, or an amino acid
64 codons but only 20 amino acids, therefore most have more than 1 codon
3 of the 64 codons are used as STOP signals (UAG,UAA,UGA); they are found at the end of every
gene and mark the end of the protein
One codon is used as a START signal (AUG): it is at the start of every protein
Universal: in all living organisms
58. How are the codons matched to amino
acids?
TACGCACATTTACGTACGCGG
DNA
AUGCGUGUAAAUGCAUGCGCC
mRNA
anti-codon
codon
tRNA UAC
Met
GCA
Arg
CAU
Val
Anti-codon = block of 3 tRNA bases
amino
acid
59. I- Initiation
mRNA
A U G C U A C U U C G
2-tRNA
G
aa2
A U
A
1-tRNA
U A C
aa1
anticodon
hydrogen
bonds codon
8/17/2022
60. mRNA
A U G C U A C U U C G
1-tRNA 2-tRNA
U A C G
aa1 aa2
A U
A
anticodon
hydrogen
bonds codon
peptide bond
3-tRNA
G A A
aa3
II-Elongation
8/17/2022
61. mRNA
A U G C U A C U U C G
1-tRNA
2-tRNA
U A C
G
aa1
aa2
A U
A
peptide bond
3-tRNA
G A A
aa3
Ribosomes move over one codon
(leaves)
62. mRNA
A U G C U A C U U C G
2-tRNA
G
aa1
aa2
A U
A
peptide bonds
3-tRNA
G A A
aa3
4-tRNA
G C U
aa4
A C U
Marga Gonfa/MSc, LL.B, PhD
Candidate/
8/17/2022
63. mRNA
A U G C U A C U U C G
2-tRNA
G
aa1
aa2
A U
A
peptide bonds
3-tRNA
G A A
aa3
4-tRNA
G C U
aa4
A C U
(leaves)
Ribosomes move over one codon
64. mRNA
G C U A C U U C G
aa1
aa2
A
peptide bonds
3-tRNA
G A A
aa3
4-tRNA
G C U
aa4
A C U
U G A
5-tRNA
aa5
8/17/2022
65. mRNA
G C U A C U U C G
aa1
aa2
A
peptide bonds
3-tRNA
G A A
aa3
4-tRNA
G C U
aa4
A C U
U G A
5-tRNA
aa5
Ribosomes move over one codon
66. III-Termination stage
At a stop codon, a release factor reads the triplet, and polypeptide synthesis
ends; the polypeptide is released from the tRNA, the tRNA is released from
the ribosome, and the two ribosomal subunits separate from the mRNA.
Polypeptide synthesis repeats until a stop codon is reached.
Chain termination requires
I. termination codons (UAA, UAG, or UGA) of mRNA
No tRNA has anticodons that pairs with the stop codons
II. release factors (RF) bind to stop codons and hydrolyzes the aminoacyl
esters liberating the peptide chain or protein, the mRNA and the ribosome
67. mRNA
A C A U G U
aa1
aa2
U
primary
structure
of a protein
aa3
200-tRNA
aa4
U A G
aa5
C U
aa200
aa199
terminator
or stop
codon
Termination
8/17/2022
68. End Product –The Protein!
The end products of protein
synthesis is a primary structure of
a protein
A sequence of amino acid bonded
together by peptide bonds
aa1
aa2 aa3 aa4
aa5
aa200
aa199
