Lf101 lecture 7 8 - tuesday 1st april 2014 -flow of genetic information & genetic code-1
-
Upload
nakul-surana -
Category
Documents
-
view
241 -
download
20
Transcript of Lf101 lecture 7 8 - tuesday 1st april 2014 -flow of genetic information & genetic code-1
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Lecture 7-81st April Tuesday 2014
Flow of genetic information: Three aspects -
Transcription, Translation&
Genetic code
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Let’s first appreciate the problem of transfer of information from DNA
(genes) to protein
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Consider the case of Sickle Cell Anemia? A serious condition in which red blood
cells can become sickle-shaped
Normal red blood cells are smooth and round. They move easily through blood vessels to carry oxygen to all parts of the body.
Sickle-shaped cells don’t move easily through blood. They’re stiff and sticky and tend to form clumps and get stuck in blood vessels.
The clumps of sickle cell block blood flow in the blood vessels that lead to the limbs and organs. Blocked blood vessel can cause pain, serious infection, and organ damage.
While the defect is seen in the protein, sickle cell anemia is produced by changes in gene sequence
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Normal and Sickled Red Blood Cells in Blood Vessels
Figure A shows normal red blood cells flowing freely in a blood vessel. The inset image shows a cross-section of a normal red blood cell with normal hemoglobin.
Figure B shows abnormal, sickled red blood cells clumping and blocking the blood flow in a blood
vessel. The inset image shows a cross-section of a sickled red blood cell with abnormal strands of
hemoglobin.
Source from http://www.nhlbi.nih.gov/health/dci/Diseases/Sca/SCA_WhatIs.html
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
• What could be the reason(s) for the wrong message from the DNA that produced a wrong protein (hemoglobin)?
• How ‘information’ encoded in the DNA of the nucleus is transferred to the cytoplasm
• How does this information ‘translate’ into protein??
Questions?
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
DNA RNA protein Transcription Translation
Replication
Reverse transcription
Central dogma of Molecular biology सि�द्धां��त
We will now explore this flow of information: that is, process
of decoding the genetic message
Flow of information Nucleic acid to
protein
Flow of information: nucleic acid to nucleic
acid
Nature of information flow
Why there is no loss of
information during
replication? How much of the information in DNA goes to
RNA??
RECAP
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Flow of genetic information
A gene is transcribed into RNA
which is then translated into the polypeptide
DNA
Transcription
RNA
Protein
Translation
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN
Gene (DNA) is a linear sequence of many nucleotides
DNA is transcribed into a linear sequence of RNA
RNA is translated into a linear sequence of amino acids – polypeptides (protein)
Entire business of flow of genetic information thus depends on constructing
(transferring information) one kind of polymer from another
DNA RNA Protein(polypeptide chain
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Transcription – Step I
Template DNA Strands unzip locally
T G C A T A G C G C A T
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Transcription – Step II
A C G T A T C G C G T A
U G C A U A G C G C A U
One of the DNA strands serve as a template and copied as mRNA
(messenger RNA)
mRNA
DNA
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
A C G T A T C G C G T A
T G C A T A G C G C A T
U G C A U A G C G C A U
DNA
RNA
mRNA is then releases
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Chemical structure of RNA
Notice the difference between ribose and deoxyribose in the figure above. In ribose, carbon atom #2 carries one hydroxyl group (colored red). In deoxyribose, carbon atom #2 carries a hyrogen atom instead of a hydroxyl group.
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Cytosine
Thymine
Uracil
Pyrimidine bases
DNA/RNA DNA RNA
In place of thymine in DNA
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Transcription
RNA polymerase RNA nucleotides
Direction of transcription
Template Strand of DNA
Newly made RNA
TC
AT C C A A T
T
GG
CC
AATTGGAT
G
U
C A U C C AA
U
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
In the nucleus, the DNA helix unzips
And RNA nucleotides line up along one strand of the DNA, following the base pairing rules
As the single-stranded messenger RNA (mRNA) peels away from the gene
The DNA strands rejoin
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Steps in transcription of a geneRNA polymerase
DNA of gene
PromoterDNA Terminator
DNA
Area shownIn Figure 10.9A
GrowingRNA
Completed RNARNApolymerase
1 Initiation
2 Elongation
3 Termination
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
T A C T T C A A A A T C
A T G A A G T T T T A G
A U G A A G U U U U A G
Transcription
Translation
RNA
DNA
Met Lys PhePolypeptide
Startcondon
Stopcondon
Strand to be transcribed
How does DNA/RNA code for protein?
Codon - a sequence of nucleotides that
codes for an amino acid
STEP III TRANSLATION
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
How can four nucleotides code for 20 amino acids?
If one nucleotide codes for one amino acid then a maximum of four amino acid could be coded
If two nucleotide code for one amino acid then a maximum of 16 amino acid could be coded
If three nucleotides code for one amino acid then a maximum of 64 codons can be generated, while the number of amino acids are only 20
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
The dictionary of genetic code (64 potential codons)
आनु�वा�न्शि�की की�ड की शब्दकी�श 5’-3’
A dictionary offers
translation from one
language to the other.
Which two languages are being
translated in a genetic
dictionary?
Why do we need this
translation?
Where does it take place?
What is the name of this
process?
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Hallmarks of genetic code
Triplet : three consecutive nucleotides code of one amino acid
Redundant : meaning not unique (there are more than one codon for most amino acids)
Universal: All organisms bacteria to human use the same genetic codes/dictionary
Comma-less: meaning consecutive codons are readout into an amino acid sequence without gaps
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
How does an universal genetic code impact Biotechnology??
What would have been the case if bacterial genetic code were to be different from human?
What do we understand when we mean when we say that genetic code is universal?
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
DNA
Messenger-RNA
Transfer RNA
Amino acid
Key players in decoding the genetic message
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Transfer RNA
Leucine
Codon
Anti-codon
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
How genetic code is readout in the cell
A C G T A T C G C G T A
T G C A T A G C G C A T DNA
3’ U G C A U A G C G C A U 5’ mRNA
5’
3’
5’G U C
3’
C A G
3’5’
tRNA
Amino acid
Anti-Codon
Codon
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Many amino acids are specified by more than one codon-degeneracy
Codons specifying the same amino acid are called synonyms
Connect the three points about genetic codes: redundancy, degeneracy and synonymous
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
CUGCUG CUCCUC
Codon-anticodon pairing of two tRNA Leu molecules
5’- 3’ 5’- 3’
Codon
GACGAC3’- 5’
Anti- codon GAGGAG3’- 5’
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Three codons direct chain termination
Three codons, UAA, UAG, and UGA signify chain termination.
They are not read by tRNAs but by proteins called release factors (RF1 and RF2 in bacteria and eRF1 in eukaryotes).
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Three Rules
Codons are read in a 5’ to 3’ direction.
Codons are non-overlapping and the message contains no gaps.
The message is translated in a fixed reading frame which is set by the initiation codon.
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
FATCATATETHERAT
Meaning and consequences of non-overlapping & comma-less reading of the triplet codons
FATATATETHERAT
Let’s consider a metaphor of a normal DNA sequence
What is the
problem here?
What is the consequenc
e?
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Mutation: a change in genetic code
1. Missense mutation: An alternation that changes a codon specific for one amino acid to a codon specific for another amino acid.
2. Nonsense or stop mutation: An alternation causing a change to a chain-termination codon.
3. Frame-shift mutation: Insertions or deletions of one or a small number of base pairs that alter the reading frame.
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
How the genetic code was cracked?
The use of artificial mRNAs and the availability of cell-free systems for carrying out protein
synthesis began to make it possible to crack the code
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Codon Assignments from Repeating Copolymers
Organic chemical and enzymatic techniques were
used to prepare synthetic poly-ribonucleotides with known
repeating sequences.
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Experimental Results:
UUU codes for phenylalanine.
CCC codes for proline.
AAA codes for lysine.
The guanine residues in poly-G firmly hydrogen bond to each other and form multistranded triple helices that do not bind to ribosomes.
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
copolymercopolymer Codons Recognized
Codons Recognized
Amino Acids Incorporated Amino Acids Incorporated
Codon Assignment
Codon Assignment
(CU)” CUC|UCU|CUC… Leucine 5’-CUC-3’
Serine UCU
(UG)” UGU|GUG|UGU… Cystine UGU
Valine GUG
(AC)” ACA|CAC|ACA… Threonine ACA
Histidine CAC
(AG)” AGA|GAG|AGA… Arginine AGA
Glutamine GAG
(AUC)” AUC|AUC|AUC… Polyisoleucine 5’-AUC-3’
(CU)” CUC|UCU|CUC… Leucine 5’-CUC-3’
Serine UCU
(UG)” UGU|GUG|UGU… Cystine UGU
Valine GUG
(AC)” ACA|CAC|ACA… Threonine ACA
Histidine CAC
(AG)” AGA|GAG|AGA… Arginine AGA
Glutamine GAG
(AUC)” AUC|AUC|AUC… Polyisoleucine 5’-AUC-3’
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
What Are Mutations?What Are Mutations?
• Changes in the nucleotide sequence of DNA
• May occur in somatic cells (aren’t passed to offspring), but could cause diseases, such as cancer
• May occur in gametes (eggs & sperm) and be passed to offspring
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Nature of point mutations
1. Missense mutation: An alternation that changes a codon specific for one amino acid to a codon specific for another amino acid.
2. Nonsense or stop mutation: An alternation causing a change to a chain-termination codon.
3. Frameshift mutation: Insertions or deletions of one or a small number of base pairs that alter the reading frame.
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Point Mutation
Change of a single nucleotide
Includes the deletion, insertion, or substitution of ONE nucleotide in a gene
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Types of Gene/Point Mutations
Substitutions
Insertions
Deletions
Frameshift
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Frameshift Mutation
Inserting or deleting one or more nucleotides
Changes the “reading frame” like changing a sentence
Proteins built incorrectly
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Gene Mutation Animation
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Problems
THE FAT CAT ATE THE BIG RAT
THE FAT ATA TET HEB IGR AT Delete C
THE FAT ATA ATE THE BIG RAT Insert A
Frame shift mutation
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
RBC Structure
of Hb
Primary sequence of Hb –first 26 amino acid
RECALL
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Example Point Mutation
• Sickle Cell disease is the result of one nucleotide substitution
• Occurs in the hemoglobin gene
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Problem
Before the true nature of the genetic coding process was fully understood, it was proposed that the message might be read in overlapping triplets. For example, the sequence of GCAUC might be read as GCA CAU AUC
G C A U C
Think of test that would negate this possibility
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Consider a gene that specified the structure of hemoglobin. Arrange the following events in the most likely sequence in which they would take place
a. Anemia is observed
b. The shape of the oxygen binding site is altered
c. An incorrect codon is transcribed into hemoglobin mRNA
d. The ovum (female gamete) receive a high radiation dose
e. An incorrect codon is generated in the DNA of the hemoglobin gene
f. A mother (an X-ray technician) accidentally steps in front of an operating X-ray generator
g. A child dies
h. The oxygen-transport capacity of the body is severely impaired
i. A wrong tRNA is attached j. Nucleotide pair substitution occurs in the DNA of the gene for hemoglobin
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
If an mRNA of human beta-globin gene is added to bacterial cell free extract then human beta globin polypeptide is formed (translated)What does this observation signify
with respect to genetic code?
Question
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Home assignment
The amino acid sequence shown in the following table was obtained from the central region of a particular polypeptide chain in the wild
type and several mutant bacterial strains
a. Wild type phe leu pro thr val thr thr arg trp
b. Mutant 1 phe leu his his gly asp asp thr val
c. Mutant 2 phe leu pro thr met thr thr arg trp
d. Mutant 3 phe leu pro thr val thr thr arg
e. Mutant 4 phe pro pro arg
f. Wild type phe leu pro ser val thr thr arg trp
1 2 3 4 5 6 7 8 9
Codon
For each mutant, say what change has occurred at the DNA level, whether the change is a base pair substitution or frame shift mutation, and in which codon the mutation occurred
Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings
Home assignment In mutant strain X of E. coli, a leucine tRNA that recognizes the codon 5’-CUG-3’ in normal cell has been so altered that is now recognizes the codon 5’-GUG-3’.
A missense mutation (lets call this mutation Y) that affects amino acid 10 of a particular protein is suppressed in mutant X cells (that is when the cells are mutant for both X and Y, which now appears wild type)
a. What mutational even has occurred in mutant X cells?
b. What amino acid would normally be present at position 10 of the protein (without the missense mutation)?
c. What amino acid is put in at position 10 if the missense mutations is not suppressed ?
d. What amino acid is put in at position 10 if the missense mutations is suppressed ?