DNA RNA protein synthesis

1. BIOSYNTHESIS OF NUCLEIC
ACIDS AND PROTEINS

2. The flow of genetic information in a typical cell
DNA
↓
RNA
↓
protein

3. Primary structure of nucleic acids

4. Two-stranded structure of DNA

5. Watson JamesCrick Francis
The double helix of DNA was discovered in 1953 by
Crick F. and Watson J. Nobel prize in 1962.

6. When replication takes place?

7. What are the principles of replication?
• Based on template;
• Complementary;
• Antiparallel;
• Two directions;
• Semi-conservative;
• Very complex.

8. Components required for
replications
• DNA molecule - template
• Origin of replication – point ORI
• Enzymes
• Nucleotides (dNTP and NTP)
• SSB proteins

9. Main enzymes required for replication
• DNA-polymerase (I, II,
III – in prokaryotes,
, ,ᵅ ᵞ ᵋ – in eukaryotes)
• Primase
• DNA-helicases
• Topoisomerase
• DNA-ligase
• Telomerase

10. Topoisomerase
Protein complexes of the
replication fork
DNA
replication

11. Reiji Okazaki provided
experimental evidence
for discontinuous DNA
synthesis

13. Details of lagging
strand synthesis

16. DNA
mRNA
Ribosome
Polypeptide
TRANSCRIPTION
TRANSLATION
TRANSCRIPTION
TRANSLATION
Polypeptide
Ribosome
DNA
mRNA
Pre-mRNA
RNA PROCESSING
(a) Bacterial cell (b) Eukaryotic cell
Nuclear
envelope

17. TRANSCRIPTION
DNA
mRNA
(a) Bacterial cell

18. TRANSCRIPTION
DNA
mRNA
(a) Bacterial cell
TRANSLATION
Ribosome
Polypeptide

19. Nuclear
envelope
DNA
Pre-mRNA
(b) Eukaryotic cell
TRANSCRIPTION

20. RNA PROCESSING
Nuclear
envelope
DNA
Pre-mRNA
(b) Eukaryotic cell
mRNA
TRANSCRIPTION

21. RNA PROCESSING
Nuclear
envelope
DNA
Pre-mRNA
(b) Eukaryotic cell
mRNA
TRANSCRIPTION
TRANSLATION Ribosome
Polypeptide

22. Nontemplate
strand of DNA
RNA nucleotides
RNA
polymerase
Template
strand of DNA
3′
3′5′
5′
5′
3′
Newly made
RNA
Direction of transcription
A
A A A
A
A
A
T
T
T
T
TTT G
G
G
C
C C
C
C
G
C CC A A
A
U
U
U
end

24. Initiation and
elongation
steps of
transcription

26. Biochemistry For Medics- Lecture
Notes
26
Post TranscriptionalPost Transcriptional
modifications ofmodifications of
pre m- RNApre m- RNA
• In prokaryotic organisms, the primary
transcripts of mRNA-encoding genes
begin to serve as translation templates
even before their transcription has been
completed.
• In all eukaryotes the primary transcripts of
mRNA-encoding genes undergo extensive
processing before they are converted to
mature functional forms

28. Post Transcriptional modifications ofPost Transcriptional modifications of
pre m- RNApre m- RNA
a) 5' Capping
• Mammalian mRNA molecules contain a 7-
methylguanosine cap structure at their 5' terminal.
• The cap structure is added to the 5' end of the newly
transcribed mRNA precursor in the nucleus prior to
transport of the mRNA molecule to the cytoplasm.
• The 5' cap of the RNA transcript is required both for
efficient translation initiation and protection of the 5'
end of mRNA from attack by 5-'3' exonucleases.
• Eukaryotic m RNAs lacking the cap are not efficiently
translated. 28

29. Post Transcriptional modifications ofPost Transcriptional modifications of
pre m- RNApre m- RNA
•The addition of the
Guanosine triphosphate
(part of the cap is
catalyzed by the nuclear
enzyme guanylyl
transferase.
•Methylation of the
terminal guanine occurs
in the cytoplasm. and is
catalyzed by guanine-7-
methyl transferase.
•S-Adenosyl methionine is the methyl group
donor.
•Additional methylation steps may occur.
The secondary methylations of mRNA
molecules, those on the 2'-hydroxy and the
•N6
of adenylyl residues, occur after the mRNA
molecule has appeared in the cytoplasm
29

30. Post Transcriptional modifications ofPost Transcriptional modifications of
pre m- RNApre m- RNA
b) Addition of poly A tail
• Poly(A) tails are added to the 3' end of mRNA molecules in
a posttranscriptional processing step.
• The mRNA is first cleaved about 20 nucleotides
downstream from an AAUAA recognition sequence
• Another enzyme, poly(A) polymerase, adds a poly(A) tail
which is subsequently extended to as many as 200 A
residues.
• The poly(A) tail appears to protect the 3' end of mRNA
from 3' 5' exonuclease attack.
• Histone and interferon's mRNAs lack poly A tail.
• After the m-RNA enters the cytosol, the poly A tail is
gradually shortened.
30

32. Post Transcriptional modifications ofPost Transcriptional modifications of
Pre m RNAPre m RNA
Removal of introns (Splicing)
• Introns or intervening sequences are the
RNA sequences which do not code for the
proteins.
• These introns are removed from the primary
transcript in the nucleus, exons (coding
sequences) are ligated to form the mRNA
molecule, and the mRNA molecule is
transported to the cytoplasm.
• The steps of splicing are as follows-
32

33. Post Transcriptional modifications ofPost Transcriptional modifications of
Pre m RNAPre m RNA
• Introns are removed from the primary transcript
in the nucleus, exons (coding sequences) are
ligated to form the mRNA molecule
33

34. Figure 17.12-1
RNA transcript (pre-mRNA)
5′
Exon 1
Protein
snRNA
snRNPs
Intron Exon 2
Other
proteins

35. Figure 17.12-2
RNA transcript (pre-mRNA)
5′
Exon 1
Protein
snRNA
snRNPs
Intron Exon 2
Other
proteins
Spliceosome
5′

36. Figure 17.12-3
RNA transcript (pre-mRNA)
5′
Exon 1
Protein
snRNA
snRNPs
Intron Exon 2
Other
proteins
Spliceosome
5′
Spliceosome
components
Cut-out
intronmRNA
5′
Exon 1 Exon 2

37. Nirenberg Marshall
decoded the genetic code.
Nobel prize, 1968

38. GENETIC
CODE -
sequence of
mononucleotides
in mRNA that
specifies the
sequence of
amino acids in
peptide chain
CODON –
mRNA triplet
base
sequence
responsible
for 1 amino
acid

39. PROPERTIES OF GENETIC CODE
1. Degenerate
2. Specific
3. Nonoverlapping
4. Without punctuation
5. Universal

40. TRANSLATION
• 1. Recognition
• 2. Initiation
• 3. Elongation
• 4. Termination

41. Formation of
aminoacyl tRNAs
by aminoacyl tRNA
synthetase.
RECOGNITION

42. Aminoacyl-tRNA
synthetase (enzyme)
Amino acid
P P P Adenosine
ATP
Figure 17.16-1

43. Aminoacyl-tRNA
synthetase (enzyme)
Amino acid
P P P Adenosine
ATP
P
P
P
P
Pi
i
i
Adenosine
Figure 17.16-2

44. Aminoacyl-tRNA
synthetase (enzyme)
Amino acid
P P P Adenosine
ATP
P
P
P
P
Pi
i
i
Adenosine
tRNA
AdenosineP
tRNA
AMP
Computer model
Amino
acid
Aminoacyl-tRNA
synthetase
Figure 17.16-3

45. Aminoacyl-tRNA
synthetase (enzyme)
Amino acid
P P P Adenosine
ATP
P
P
P
P
Pi
i
i
Adenosine
tRNA
AdenosineP
tRNA
AMP
Computer model
Amino
acid
Aminoacyl-tRNA
synthetase
Aminoacyl tRNA
(“charged tRNA”)
Figure 17.16-4

46. Components of a 70S prokaryotic ribosome

47. tRNA
molecules
Growing
polypeptide Exit tunnel
E P
A
Large
subunit
Small
subunit
mRNA
5′
3′
(a) Computer model of functioning ribosome
Exit tunnel Amino end
A site (Aminoacyl-
tRNA binding site)
Small
subunit
Large
subunit
E P A
mRNA
E
P site (Peptidyl-tRNA
binding site)
mRNA
binding site
(b) Schematic model showing binding sites
E site
(Exit site)
(c) Schematic model with mRNA and tRNA
5′ Codons
3′
tRNA
Growing polypeptide
Next amino
acid to be
added to
polypeptide
chain
Figure 17.17

48. Figure 17.17a
tRNA
molecules
Growing
polypeptide Exit tunnel
E P A
Large
subunit
Small
subunit
mRNA
5′
3′
(a) Computer model of functioning ribosome

49. Figure 17.17b
Exit tunnel
A site (Aminoacyl-
tRNA binding site)
Small
subunit
Large
subunit
P A
P site (Peptidyl-tRNA
binding site)
mRNA
binding site
(b) Schematic model showing binding sites
E site
(Exit site)
E

50. Figure 17.17c
Amino end
mRNA
E
(c) Schematic model with mRNA and tRNA
5′ Codons
3′
tRNA
Growing polypeptide
Next amino
acid to be
added to
polypeptide
chain

51. Initiation of protein
biosynthesis in
prokaryotes.

52. Elongation of the Polypeptide Chain
• During the elongation stage, amino acids
are added one by one to the preceding
amino acid at the C-terminus of the
growing chain
• Each addition involves proteins called
elongation factors and occurs in three
steps: codon recognition, peptide bond
formation, and translocation
• Translation proceeds along the mRNA in a
5′ to 3′ direction

53. Amino end of
polypeptide
mRNA
5′
E
P
site
A
site
3′

54. Amino end of
polypeptide
mRNA
5′
E
P
site
A
site
3′
E
GTP
GDP + P i
P A

55. Amino end of
polypeptide
mRNA
5′
E
P
site
A
site
3′
E
GTP
GDP + P i
P A
E
P A
Elongation
1) Positioning of
aminoacyl-tRNA
in the A site
2) Formation of the
peptide bound
(enzyme – peptidyl
transferase)
3) Translocation

56. Amino end of
polypeptide
mRNA
5′
E
A
site
3′
E
GTP
GDP + P i
P A
E
P A
GTP
GDP + P i
P A
E
Ribosome ready for
next aminoacyl tRNA
P
site

57. Termination of
translation in
prokaryotes

59. POSTTRANSLATIONAL MODIFICATION
1) Preparing of proteins for different functions
2) Direction of proteins to different locations (targeting)
1. Proteolytic cleavage
2. Hydroxylation
3. Glycosilation
4. Phosphorilation
5. Lipophilic modification

60. The operon model (by Jacob and Monod)

61. Some inhibitors of transcription

62. Some antibiotics
that act by
interfering with
protein biosynthesis