2. Basic components of RNA
Ribonucleic acid
consists of following
basic components
1- Ribose sugar
2- Phosphate in
diester linkage
4-Nitrogenous
base pairs-
Purines- adenine,
guanine
Pyrimidines- cytocine,
uracil
3. Primary structure of RNA
Although there are
multiple types of RNA
molecules, the basic
structure of all RNA is
similar.
Each kind of RNA is a
polymeric molecule
made by stringing
together individual
ribonucleotides,
always by adding the
5'-phosphate group
of one nucleotide
onto the 3'-hydroxyl
group of the previous
4. Secondary structure of RNA
Single-stranded RNA can
also form many
secondary structures in
which a single RNA
molecule folds over and
forms hairpin loops,
stabilized by
intramolecular hydrogen
bonds between
complementary bases.
Such base-pairing of RNA
is critical for many RNA
functions, such as the
ability of tRNA to bind to
the correct sequence of
mRNA during translation
5. DNA can replicate or
undergo transcription
Replication-it is process by which DNA copies itself
to produce identical daughter molecules of DNA.
DNA is the reserve bank of genetic information.
Transcription-transcription results in the formation
of one single-stranded RNA molecule.
6. DNA RNA
Structure Double
Stranded
Single Stranded
Bases- Purines Adenine (A) Adenine (A)
Guanine (G) Guanine (G)
Bases -
Pyrimidines
Cytosine (C) Cytosine (C)
Thymine (T) Uracil (U)
Sugar Deoxyribose Ribose
Differences between DNA and RNA:
RNA’s JOB= Make Proteins!!
7. Types of RNA
1) messenger RNA (mRNA)- carries
instructions from the DNA in the
nucleus to the ribosome
8. Types of RNA
2) ribosomal RNA (rRNA)-
combines with proteins to
form the ribosome (proteins
made here)
3) transfer RNA (tRNA)-
transfers each amino acid to
the ribosome as it is specified
by coded messages in mRNA
during the construction of a
protein
9. Types of RNA
4 ) snRNA – small nuclear RNA
5) snoRNA- small nucleolar RNA
6) scRNA- small cytoplasmic RNA
7) micro- RNAs,miRNA, small interfering RNAs
Present in eukaryotes only.
10. Protein Synthesis Overview
There are two steps to making
proteins (protein synthesis):
1) Transcription (nucleus)
DNA RNA
2) Translation (cytoplasm)
RNA protein
11. DNA
Transcription
RNA
Translation
Protein
Conventional concept
Genome
Transcription
Transcriptome
Translation
Proteome
Current concept,
Bioinformatics era
16. TRANSCRIPTION
It is a process by which RNA is synthesize from
DNA. The genetic information stored in DNA is
expressed through RNA.
One of the two strands of DNA serves as
Template and produces working copies of RNA
molecules. The other DNA strand which does not
participate in in transcription is referred to as
coding strand or sense strand or non-template
strand.
17. Transcription
RNA Editing: Before the mRNA leaves the
nucleus, it is called pre-mRNA or (hnRNA)
heterogeneous nuclear RNA and it gets
“edited.” Parts of the pre-mRNA that are not
involved in coding for proteins are called introns
and are cut out. The remaining mRNA pieces
are called exons (because they are expressed)
and are spliced back together to form the
mRNA.
Then the final mRNA leaves the nucleus through
the nuclear pores and enters the cytoplasm
headed to the ribosome.
18. Transcription
1) Transcription begins when the
enzyme RNA polymerase binds to
DNA at a promoter region.
Promoters are signals in DNA that
indicate to the enzyme where to bind
to make RNA.
2) The enzyme separates the DNA
strands by breaking the hydrogen
bonds, and then uses one strand of
DNA as a template from which
nucleotides are assembled into a
strand of RNA.
19. Transcription
3) RNA polymerase pairs up free
floating RNA nucleotides with
DNA template and joins the
nucleotides together to form the
backbone of the new mRNA
strand.
4) When mRNA hits a termination
sequence, it separates from the
DNA
20. Steps of transcription
Initiation
Elongation
Termination
post – transcriptional modifications
The RNAs produced during transcription are
called primary mRNA transcripts. They undergo
many alterations- terminal base additions, base
modifications, splicing etc. This process is
required to convert RNA into active form.
Enzyme involved mainly is - ribonucleases.
42. The conventional numbering system of promoters
Bases preceding
this are numbered
in a negative
direction
There is no base
numbered 0
Bases to the right are
numbered in a
positive direction
Most of the promoter region is
labeled with negative numbers
43. Promoter sites
In eukaryotes promoter DNA bases sequences known as HOGNESS BOX or
TATA BOX located on the left about 25 nucleotides away(upstream) from
the starting site of mRNA synthesis. Second site of recognition between 70 to
80 nucleotides upstream known as CAAT BOX.
Coding strand 5’ GGCCAATC ATATAA 3’
Template strand 3’ 5’
-70 bases -25 bases (coding region)
Start of transcription
45. Factors that control gene expression can be divided
into two types, based on their “location”
cis-acting elements
DNA sequences that exert their effect only over a
particular gene
Example: TATA box
trans-acting elements
Regulatory proteins that bind to such DNA sequences
Sequences of Eukaryotic
Structural Genes
47. Usually
an
adenine
The core promoter is relatively short
It consists of the TATA box
Important in determining the precise start point for transcription
The core promoter by itself produces a low level of
transcription
This is termed basal transcription
48. Regulatory elements affect the binding of RNA polymerase
to the promoter
They are of two types
Enhancers
Stimulate transcription
Silencers
Inhibit transcription
They vary widely in their locations, from –50 to –100
region
49. RNA polymerases
RNA polymerase I- synthesis of precursors of large
ribosomal RNAs.
RNA polymerases II- synthesizes the precursors for
mRNAs and small rRNAs.
RNA polymerases III- formation of tRNAs and
small rRNAs.
54. 12-26
Similar to the
synthesis of DNA
via DNA polymerase
Figure 12.8
On average, the rate of
RNA synthesis is about 43
nucleotides per second!
55. ‘promoter’ Protein coding
Difference in gene structure between
- prokaryote
- eukaryote
core
‘promoter’
An important difference between prokaryotes and eukaryotes
is that eukaryotes’ genes are not split into intons and exons.
In eukaryotes is the DNA coding protein are, Therefore, exons
eventually end up in the mRNA
intron
exons
56. Pre-mRNA
Transcription start, elongation, termination and RNA
processing in eukaryotes
: coding protein
: non-coding protein: ‘leader’ and ‘trailer’
CAP
CAP (poly A tail)
The longest gene in human genome is more than 1.500.000 base pares
(bp) and the mRNA is ~ 7000 nt.
‘promoter’
intron
exons
GENE
mRNA
AAAAAAAAAAA
57. TERMINATION
Transcription stops by termination signals. Two
types of termination identified.
Rho depended- specific protein Rho factor,
binds to the growing RNA, acts as ATPase and
terminates transcription and releases RNA.
Rho independent – formation of hairpins of newly
synthesized RNA.this occurs due to presence of
palindromes. It is word that reads alike forward
and backwards, like madam, motor. Presence of
palindromes in DNA base sequence work as
termination zone. Newly synthesize RNA folds to
form hairpins due to complimentary base
pairing, and termination occurs.
58. coding sequences, called exons, are interrupted by
intervening sequences or introns
Transcription produces the entire gene product
Introns are later removed or excised
Exons are connected together or spliced
This phenomenon is termed RNA splicing
It is a common genetic phenomenon in eukaryotes
Occurs occasionally in bacteria as well
post transcriptional RNA
modification
59. Aside from splicing, RNA transcripts can be modified
in several ways
For example
Trimming of rRNA and tRNA transcripts
5’ Capping and 3’ polyA tailing of mRNA transcripts
y
RNA MODIFICATION
62. The spliceosome is a large complex that splices
pre-mRNA
It is composed of several subunits known as
snRNPs (pronounced “snurps”)
Each snRNP contains small nuclear RNA and a set of
proteins. Or small nuclear ribonucloprotein particle.
Types of snRNPs are U1,U2,U3,U4,U5,U6.
Pre-mRNA Splicing
63. The subunits of a spliceosome carry out several
functions
1. Bind to an intron sequence and precisely recognize
the intron-exon boundaries
2. Hold the pre-mRNA in the correct configuration
3. Catalyze the chemical reactions that remove introns
and covalently link exons
Pre-mRNA Splicing
66. One benefit of genes with introns is a phenomenon
called alternative splicing
A pre-mRNA with multiple introns can be spliced in
different ways
This will generate mature mRNAs with different
combinations of exons
This variation in splicing can occur in different cell
types or during different stages of development
Intron Advantage?
67. The biological advantage of alternative splicing is
that two (or more) polypeptides can be derived
from a single gene
This allows an organism to carry fewer genes in its
genome
Intron Advantage?
68. Most mature mRNAs have a 7-methyl guanosine
covalently attached at their 5’ end
This event is known as capping
Capping occurs as the pre-mRNA is being
synthesized by RNA pol II
Usually when the transcript is only 20 to 25 bases long
Capping: marking 5’ends of mRNAs
69. The 7-methylguanosine cap structure is recognized
by cap-binding proteins
Cap-binding proteins play roles in the
Movement of some RNAs into the cytoplasm
Early stages of translation
Splicing of introns
Function of Capping
70. Most mature mRNAs have a string of adenine
nucleotides at their 3’ ends
This is termed the polyA tail
The polyA tail is not encoded in the gene sequence
It is added enzymatically after the gene is completely
transcribed
The 3’ end of a mRNA: Tailing
87. RNA Polymerase binds to
the promoter region.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
88. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
89. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
90. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
91. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
92. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
93. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
94. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
95. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
96. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
97. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymerase
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
98. RNA Polymerase reads the DNA
and creates the mRNA strand.
RNA
Polymeras
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Coding Region
mRNA Strand
99. mRNA leaves the nucleus and enters
the cytoplasm.
RNA
Polymeras
Guanine
Cytosine
Thymine
Adenine
Uracil
Start Codon Stop CodonCoding Region
mRNA Strand
Termination Sequ
108. The Genetic Code
Proteins (polypeptides) are long chains of amino acids that
are joined together.
There are 20 different amino acids.
The structure and function of proteins are determined by the
order in which different amino acids are joined together to
produce them.
The four bases (letters) of mRNA
(A, U, G, and C) are read three
letters at a time (and translated) to
determine the order in which
amino acids are added to a
protein.
109. AMINO ACIDS
Amino acids are organic solvents.
Have two functional groups –NH₂ and
-COOH group.
The amino group is basic while carboxylic group is
acidic in nature.
Soluble in water but insoluble in organic solvents e.g.
chloroform,acetone,ether,etc.
All amino acids which make up proteins are L-α-
aminoacids.
110.
111.
112.
113.
114. Semi-essential aminoacids.
These include Arginine and
Histidine.These are growth
promoting factors since they are not
synthesized in sufficient quantity
during growth.
SELENOCYSTEINE- the 21st amino
acid.
115. The Genetic Code
A codon consists of three
consecutive nucleotides
that specify a single
amino acid that is to be
added to the polypeptide
(protein).
117. Some codons do
not code for
amino acids; they
provide
instructions for
making the
protein.
More than one
codon can code
for the same
amino acid.
118. All organisms use the same genetic
code (A,T,C,G).
This provides evidence that all
life on Earth evolved from a
common origin.
119.
120. Cracking the Code
This picture shows the amino
acid to which each of the 64
possible codons corresponds.
To decode a codon, start at
the middle of the circle and
move outward.
Ex: CGA
Arginine
Ex: GAU
Aspartic Acid
121. Translation
Translation takes place
on ribosomes, in the
cytoplasm.
The cell uses information
from messenger RNA
(mRNA) to produce
proteins, by decoding the
mRNA message into a
polypeptide chain
(protein).
122. Stapes of protein synthesis
1) requirements of the components- amino
acids, ribosome, mRNA,tRNA, ATP
2)activation of amino acids
3)protein synthesis proper
4) chaperones and protein folding
5) post – translational modifications.
148. Messenger RNA (mRNA)
1) The mRNA that was transcribed from DNA
during transcription, leaves the cell’s nucleus and
enters the cytoplasm.
149. Transfer RNA(tRNA)
2) The mRNA enters the cytoplasm and attaches to a ribosome at the
AUG, which is the start codon. This begins translation.
3) The transfer RNA (tRNA) bonds with the correct amino acid and
becomes “charged.” (in the cytoplasm)
4) The tRNA carries the amino acid to the ribosome.
Each tRNA has an anticodon whose bases are complementary to a
codon on the mRNA strand. (The tRNA brings the correct amino
acid to the ribosome.)
Ex: The ribosome positions the start
codon to attract its anticodon, which
is part of the tRNA that binds
methionine.
The ribosome also binds the next
codon and its anticodon.
150. The Polypeptide “Assembly Line”
5) The ribosome moves along the mRNA and adds more amino
acids to the growing polypeptide or protein
The tRNA floats away,
allowing the ribosome to bind
to another tRNA.
The ribosome moves along the
mRNA, attaching new tRNA
molecules and amino acids.
151. Completing the Polypeptide
6) The process continues
until the ribosome
reaches one of the three
stop codons on the
mRNA, and then the
ribosome falls off the
mRNA.
7) The result is a
polypeptide chain or
protein that is ready for
use in the cell.
