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Signals and Systems in
Biology
All cells come from pre-existing cell - Rudolf Vircow
A cell is the basic building unit of life
A cell is a self replicating body capable of its own sustenance and maintenance.
Mitocondria and Chloroplast – The kitchen of the cell.
Nucleus – Contains information for replication i.e. the genetic material.
A typical prokaryotic cell
A typical plant cell
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A typical mammalian cell
Figure 1-30 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
Figure 1-21 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
Biological Viruses – Lie at the borderline between living and non-living
Tobacco Mosaic Virus
A bacteriophage (bacteria eater)
Human Immunodeficiency Virus (HIV)
Figure 2-17 Molecular Biology of the Cell (© Garland Science 2008)
Genetic Material : DNA or De-oxy ribonucleic acid
Figure 1-2a Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
There are four types of bases
Adenine (A)
Thymine (T)
Guanine (G)
Cytosine (C)
The phosphate rich back bone of DNA makes it electro-negative,
hence having affinity for positive charged molecules (eg. proteins).
Figure 1-2b Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
Chemical structure of a single strand of DNA
Figure 2-28 Molecular Biology of the Cell (© Garland Science 2008)
Adenine always pairs with Thymine via 2 hydrogen bonds.
Guanine always pairs with Cytosine via 3 hydrogen bonds.
Figure 1-2c Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
DNA exists in a helix –
proposed and proved by
Watson, Crick and Franklin
Helix imparts effective
packaging of the genetic
material inside the miniscule cell.
Figure 1-2d,e Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
A typical .fna file downloadable from NCBI
Figure 4-7 Molecular Biology of the Cell (© Garland Science 2008)
Human Chromosomes
Figure 4-10 Molecular Biology of the Cell (© Garland Science 2008)
Life began in a RNA world
because RNA can act as genetic material as well as an enzyme (ribozymes)
Figure 6-98 Molecular Biology of the Cell (© Garland Science 2008)
RNA – Ribonucleic acid
Figure 6-4a Molecular Biology of the Cell (© Garland Science 2008)
In RNA thymine is replaced by uracil base.
Uracil base pairs with Adenine via 2 H-bonds
Figure 6-4b Molecular Biology of the Cell (© Garland Science 2008)
Chemical structure of RNA
Figure 6-4c Molecular Biology of the Cell (© Garland Science 2008)
Table 6-1 Molecular Biology of the Cell (© Garland Science 2008)
mRNA : messenger RNA
Figure 6-22a Molecular Biology of the Cell (© Garland Science 2008)
rRNA : ribosomal RNA
The RNA which is bound with ribosomes in the cell cytoplasm.
It is usually a co-translation product.
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tRNA- Transfer RNA
Figure 6-52a Molecular Biology of the Cell (© Garland Science 2008)
Proteins
Amino acids are the building blocks of proteins.
There are twenty amino acids.
Essential amino acids are those that cannot be
synthesized by the organism de novo.
For humans they are Phe, Val, Thr, Trp, Ile, Leu, Met, Lys and His.
Figure 3-2 Molecular Biology of the Cell (© Garland Science 2008)
Amino acids are the basic units of proteins
The ‘H’ is replaced by various groups to generate other
19 amino acids.
All the amino acids carry both positive and negative
charges, hence they are termed as Zwitter ions.
Bond between two amino acids is known as a peptide bond
Proteins are also termed as polypeptides. In biological systems
synthesis of proteins happens in N terminus→C terminus direction.
http://www.ucl.ac.uk/~sjjgsca/ProteinStructure.html
Four levels of protein structure
αHelix
β-Pleated sheets
Ramachandran Plot
Torsion in Phi and Psi angles can occur only in some permissable limits
i.e only certain combinations of these two angles are possible.
These limits were first mapped by G.N. Ramachandran in the 1960s.
Figure 3-3a Molecular Biology of the Cell (© Garland Science 2008)
Ramachandran Plot
Figure 3-3b Molecular Biology of the Cell (© Garland Science 2008)
Broadly proteins can be classified into four categories
Central Dogma in Molecular Biology
Some viruses were discovered to have RNA as genetic
material and among them few replicate forming a DNA
intermediate (Reverse Transcription).
Figure 6-2 Molecular Biology of the Cell (© Garland Science 2008)
The transfer of information from DNA to protein
A nascent RNA is highly unstable.
Post-transcriptional modifications
confers stability to the RNA.
Figure 3-15 Molecular Biology of the Cell (© Garland Science 2008)
Transport of a modified RNA from nucleus to cytoplasm
Figure 6-40 Molecular Biology of the Cell (© Garland Science 2008)
Gene coding and non-coding region
Figure 1-45 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
Following codons code for corresponding amino acids.
This code is followed in every living organism on earth without ANY exception.
The genetic code is degenerate: 64 codons code for 20 amino acids.
Figure 6-50 Molecular Biology of the Cell (© Garland Science 2008)
Wobble hypothesis : Rules of base pairing are relaxed at the third position
Wobble rule makes the genetic code degenerate
i.e. many codons code for a single amino acid.
Figure 6-53 Molecular Biology of the Cell (© Garland Science 2008)
Open Reading Frame (ORF)- Part of reading frame
with no stop codon
Figure 6-51 Molecular Biology of the Cell (© Garland Science 2008)
Translation
Figure 6-66 (part 1 of 4) Molecular Biology of the Cell (© Garland Science 2008)
Translation
Figure 6-66 Molecular Biology of the Cell (© Garland Science 2008)
Termination of Translation
Figure 6-74 (part 2 of 3) Molecular Biology of the Cell (© Garland Science 2008)
Folding of proteins occur co-translationally
Figure 6-84 Molecular Biology of the Cell (© Garland Science 2008)
Biologically active protein is made after post-translational
modifications of a polypeptide.
Figure 6-82 Molecular Biology of the Cell (© Garland Science 2008)
Flow of information from DNA to proteins
To ensure the faithful decoding of
information from DNA to proteins, there are
several levels of regulation both at
transcription and translational level.
Figure 6-97 Molecular Biology of the Cell (© Garland Science 2008)
Replication of DNA
Figure 1-2 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
DNA replication is semi-conservative – Meselson and Stahl, 1958
Figure 1-3 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
Process of replication of DNA is not identical
on both the strands.
Figure 5-21 Molecular Biology of the Cell (© Garland Science 2008)
DNA replication initiates on a
oligonucleotide called primer
Figure 5-3 Molecular Biology of the Cell (© Garland Science 2008)
Figure 5-26 Molecular Biology of the Cell (© Garland Science 2008)
Mechanisms to ensure fidelity in replication
Figure 5-48 Molecular Biology of the Cell (© Garland Science 2008)
Table 4-1 Molecular Biology of the Cell (© Garland Science 2008)