Transcript Chapters 11 & 14

RNA
YUSRON SUGIARTO, STP, MP, MSc
1
Central Dogma of
Molecular Biology
• The flow of information in the cell starts at
DNA, which replicates to form more DNA.
Information is then ‘transcribed” into RNA,
and then it is “translated” into protein. The
proteins do most of the work in the cell.
Structure of RNA
A. Chain of nucleotides like DNA
B. Parts of an RNA nucleotide
1. 5 carbon sugar: ribose
2. phosphate group
3. nitrogen base
O
C
5’ end
HN
C
H2N-C
C
5’
HO-CH2
N
N
DNA is a polymer of
2’-deoxyribonucleotides
CH
N
NH2
O
4’
G
3’
O
O P O
C
1’
CH
N
2’
O
CH2
O
C
C
CH
N
O
O
C
 2’-deoxyribose sugars
 Phosphodiester linkages
O
O P O
C
O
CH2
O
 4 Bases
purines: adenine & guanine
pyrimidines: cytosine & thymine
O
O P O
N
NH2
C
N
N
C
HC
C
N
CH2
O
O
3’
3’ end
T
CH
O
 Directional chain (5’ to 3’)
CH3
C
HN
O-PO32
A
CH
N
O
C
5’ end
HN
C
H2N-C
C
5’
HO-CH2
N
N
N
NH2
3’
O
O P O
C
1’
2’
OH
 Phosphodiester linkages
CH
N
O
CH2
O
 ribose sugars
RNA is a polymer of
ribonucleotides
CH
O
4’
G
C
C
CH
N
O
O
O
O P O
C
OH
HN
CH
C
CH
O
CH2
O
N
NH2
O
C
 Directional chain (5’ to 3’)
 4 Bases
purines: adenine & guanine
pyrimidines: cytosine & uracil
U
N
O
N
C
HC
C
N
OH
N
O P O
CH2
O
CH
O
3’
3’ end
A
O-PO32
OH
C. The RNA bases
1. Purines
a. Adenine (A)
b. Guanine (G)
2. Pyrimidines
a. Cytosine (C)
b. Uracil (U)
D. Shape of the molecule: several
shapes, but all are single stranded
E. Differences between DNA and
RNA
1. Different sugars:
DNA=deoxyribose,
RNA=ribose
2. Different base: DNA=thymine,
RNA=uracil
3. Different shape: DNA=double
helix, RNA=single strand
F. Types of RNA
1. Messenger RNA (mRNA): long,
single stranded molecule that
carries DNA message to the
ribosomes
2. Transfer RNA (tRNA): small
clover-leaf shaped molecules that
pick up amino
acids and take
them to the ribosomes
3. Ribosomal RNA (rRNA): makes
up the structure of ribosomes along
with proteins
rRNA
• rRNA—ribosomal
RNA
– Two subunits
• Ribosome “reads”
mRNA and produces
a polypepide
3 Types of RNA
• 1.mRNA
– Messenger RNA
• Single strand
• Serves as a template
(pattern for
translation)
3 Types of RNA
• 2. tRNA
– Transfer RNA
• 20+ types of tRNA
• Cloverleaf shape
• Each tRNA is specific
for an amino acid
3 Types of RNA
• 3. rRNA
– Ribosomal RNA
• Globular
• 2 parts compose the
ribosome
• Where are they
made?
F.
The roles of RNA
1. RNA is not the genetic material and
does not need to be capable of
serving as a template for its own
replication.
2. RNA functions as the intermediate,
the mRNA, between the gene and
the protein-synthesizing machinery.
3. RNA functions as an adaptor, the
tRNA, between the codons in the
mRNA and amino acids.
F.
The roles of RNA
4. RNA also play a structural role, as in
the case of the RNA components of the
ribosome.
5. RNA is as a regulatory molecule,
which through sequence
complementarity binds to, and
interferes with the translation of,
certain mRNAs.
6. Some RNAs are enzymes that
catalyze essential reactions in the cell.
The phosphate groups of
DNA and RNA are
negatively charged
5’
HO-CH2
N
O
O
M+
O P O
CH2
O
N
O
O
A phosphodiester group has a
pKa of about 1, and so will
always be ionized and negatively
charged under physiological
conditions (pH ~7).
Nucleic acids require counterions
such as Mg2+, polyamines,
histones or other proteins to
balance this charge.
O P O
M+
CH2
O
N
O
O
O P O
M+
CH2
O
N
O
3’
O-PO32
M+
Transcription
A. Transcription: the process in which
DNA makes a complementary
copy of mRNA
B. Steps of transcription
1. DNA untwists and bases
separate
2. Only a small section of the
DNA is involved and only one
strand acts as the template
3. RNA polymerase adds RNA
nucleotides in the correct order as
indicated by the DNA molecule
4. Base pairing rules apply
a. If DNA has a T, RNA will
match by adding A
b. If DNA has an A, RNA will
match by adding U
c. If DNA has a C, RNA will
match by adding G
d. If DNA has a G, RNA will
match by adding C
5. Fill in correct mRNA sequence
DNA: A T G C C T A G A
RNA: U A C G G A U C U
Most RNA molecules consist of a single strand that folds
back on itself to form double-helical regions
single
strands
bulge
A
hairpin
internal
loop
CGU
A-form
double
helix
In RNA, G pairs with C
and A pairs with U.
GCA
The loops and
hairpins have few
or no base-pairs
Transcription
• Enzyme: RNA
polymerase (3 kinds in
eukaryotes)
• “unzips” DNA and
adds RNA nucleotides
in the 5’ 3” direction
Transcription
• Promotor
– Site where the
polymerase attaches
• Termination site
– Site where
transcription ends
• Transcription Unit
– The stretch of DNA
transcribed
Transcription
• In eukaryotes, the
mRNA is modified
after transcription
• A 5’ cap is added
(guanine nuicleotide)
• Poly A tail (adenine)
• 50-250 nucleotides
long
Transcription Graphics
RNA Processing
A. There are large sections of
RNA molecules that are not
used in making protein. These
must be cut out before the
RNA leaves the nucleus
B. Sections that are cut out (not
used to make the protein) are
called introns
C. Sections that are used to make
the protein are called exons
(they are expressed)
D. Some parts of RNA molecules
may be exons when one protein
is made and introns when
another protein is made
The Genetic Code
A. Tells the cell how to assemble a
protein
B. Proteins determine the structure
and function of organisms
C. Proteins are made of amino acids
D. The bases in mRNA (as made from
DNA) determine what amino acids
will be assembled into a protein
E. 20 amino acids can be
assembled into thousands of
proteins
F. This works similar to the way
letters are assembled to make
words
- 26 letters in English alphabet
make thousands of words
G. Codon: a sequence of 3 bases in
mRNA that codes for 1 amino
acid
1. Examples
GUG = valine
GUA = valine
GUC = valine
GAC = aspartic acid
GAU = aspartic acid
UCU = serine
UCC = serine
UCG = serine
Which base could vary and still
stand for the same amino acid?
- 3rd base
2. The genetic code is
redundant: more than 1 codon
can stand for 1 amino
acid
3. The genetic code is NOT
ambiguous: 1 codon cannot
stand for more
than 1
amino acid
4. Special codons
AUG = methionine = “start” =
the first codon of every protein
UAA = stop
UAG = stop
UGA = stop – these end a protein
Fill in the chart…
mRNA codon
Amino acid
AAG
Lysine
CGU
Argenine
GGG
Glycine
Translation
A. Translation: the process in which
the mRNA message is decoded
and a protein is made.
B. Steps in translation
1. mRNA made in the nucleus
leaves and travels to a
ribosome
2. mRNA attaches to a
ribosome
3. The ribosome reads the first
codon, which is always AUG
4. A tRNA that has a sequence
of three complementary bases to
mRNA brings in the appropriate
amino acid. The complementary
bases on tRNA are called an
anticodon.
5. The ribosome reads the second
codon and a tRNA with a
matching anticodon brings in a
second amino acid
6. The ribosome joins the two
amino acids with a linkage
that is called a peptide bond
7. The ribosome moves down
and reads the next codon
8. tRNA molecules keep bringing in the
appropriate amino acids
9. The process continues until a “stop”
codon is reached
10. The polypeptide leaves the
ribosome and folds to become a
protein
Translation
• RNA protein
• Structure of a
ribosome
– Protein and rRNA
– Most common form
of RNA
– Ribosomes are
formed in the
nucleolus
Translation
•
Three stages of
translation
1. Initiation
2. Elongation
3. Termination
Initiation
• Small ribosomal
subunit binds to both
the mRNA and the
tRNA
• Large ribosomal
subunit attaches
Elongation
Exit
site
• Codon recognition--mRNA and
tRNA form hydrogen bonds at
the “A” site of the ribosome
• Peptide bond forms between
amino acid at the “A” site and
the growing polypeptide at the
“P” site
• Translocation
– Ribosome moves the tRNA
with polypeptide from the
“A” to the “P”
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Termination
• Translation continues
until “stop” codon on
mRNA—UAA, UAG,
or UGA
• Polyribosomes
• Multiple ribosomes
translating the same
rRNA (polysomes)
Genetic Code Table
codons
• Universal for almost
all organisms
– P. 308 in text
– Use it to decode
the base sequence
on the next slide
Transcription and Translation in Cells
Prokaryotic Cell
Eukaryotic Cell
48
THANK YOU
YUSRON SUGIARTO, STP, MP, MSc
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