Lecture 2Molecular Biology Primer

Saurabh Sinha

Heredity and DNA

• Heredity: children resemble parents– Easy to see– Hard to explain

• DNA discovered as the physical (molecular)carrier of hereditary information

Life, Cells, Proteins

• The study of life ⇔ the study of cells• Cells are born, do their job, duplicate, die• All these processes controlled by proteins

Protein functions• “Enzymes” (catalysts)

– Control chemical reactions in cell– E.g., Aspirin inhibits an enzyme that produces the

“inflammation messenger”

• Transfer of signals/molecules between andinside cells– E.g., sensing of environment

• Regulate activity of genes

DNA

• DNA is a molecule: deoxyribonucleic acid

• Double helical structure (discovered byWatson, Crick & Franklin)

• Chromosomes are densely coiled andpacked DNA

SOURCE: http://www.microbe.org/espanol/news/human_genome.asp

Chromosome

DNA

The DNA Molecule

G -- CA -- TT -- AG -- CC -- GG -- CT -- AG -- CT -- AT -- AA -- TA -- TC -- GT -- A

≡

Base = Nucleotide

5’

3’

Base pairing property

Protein

• Protein is a sequence of amino-acids•• 20 possible amino acids

• The amino-acid sequence “folds” into a 3-Dstructure called protein

Protein Structure

Protein

DNA

The DNA repair protein MutY (blue) bound to DNA (purple).

PNAS cover, courtesy A

mie Boal

SRC:http://www.biologycorner.com/resources/DNA-RNA.gif

Cell

From DNA to Protein: In picture

From DNA to Protein: In words1. DNA = nucleotide sequence

• Alphabet size = 4 (A,C,G,T)

2. DNA → mRNA (single stranded)• Alphabet size = 4 (A,C,G,U)

3. mRNA → amino acid sequence• Alphabet size = 20

4. Amino acid sequence “folds” into 3-dimensional molecule called protein

What about RNA ?

• RNA = ribonucleic acid• “U” instead of “T”• Usually single stranded• Has base-pairing capability

– Can form simple non-linear structures• Life may have started with RNA

DNA and genes

• DNA is a very “long” molecule– If kept straight, will cover 5cm (!!) in human cell

• DNA in human has 3 billion base-pairs– String of 3 billion characters !

• DNA harbors “genes”– A gene is a substring of the DNA string– A gene “codes” for a protein

Genes code for proteins

• DNA → mRNA → protein can actuallybe written as Gene → mRNA → protein

• A gene is typically few hundred base-pairs (bp) long

Transcription

• Process of making a single stranded mRNAusing double stranded DNA as template

• Only genes are transcribed, not all DNA

• Gene has a transcription “start site” and atranscription “stop site”

Step 1: From DNA to mRNA

Transcription

SOURCE: http://www.fed.cuhk.edu.hk/~johnson/teaching/genetics/animations/transcription.htm

Translation

• Process of making an amino acid sequencefrom (single stranded) mRNA

• Each triplet of bases translates into oneamino acid

• Each such triplet is called “codon”

• The translation is basically a table lookup

The

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Step 2: mRNA to Amino acid sequence

Translation

SOURCE: http://bioweb.uwlax.edu/GenWeb/Molecular/Theory/Translation/trans1.swf

Gene structure

SOURCE: http://www.wellcome.ac.uk/en/genome/thegenome/hg02b001.html

Gene structure

• Exons and Introns– Introns are “spliced” out, and are not part of

mRNA

• Promoter (upstream) of gene

Gene expression

• Process of making a protein from agene as template

• Transcription, then translation

• Can be regulated

Gene Regulation

• Chromosomal activation/deactivation• Transcriptional regulation• Splicing regulation• mRNA degradation• mRNA transport regulation• Control of translation initiation• Post-translational modification

GENE

ACAGTGA

TRANSCRIPTIONFACTOR

PROTEIN

Transcriptional regulation

GENE

ACAGTGA

TRANSCRIPTIONFACTOR

PROTEIN

Transcriptional regulation

The importance of generegulation

Genetic regulatory network controlling the development of the body plan of the sea urchin embryoDavidson et al., Science, 295(5560):1669-1678.

• That was the “circuit” responsible fordevelopment of the sea urchin embryo

• Nodes = genes• Switches = gene regulation

Genome• The entire sequence of DNA in a cell

• All cells have the same genome– All cells came from repeated duplications starting

from initial cell (zygote)

• Human genome is 99.9% identical amongindividuals

• Human genome is 3 billion base-pairs (bp) long

Genome features• Genes

• Regulatory sequences

• The above two make up 5%of human genome

• What’s the rest doing?– We don’t know for sure

• “Annotating” the genome– Task of bioinformatics

Some genome sizesOrganism Genome size (base pairs)Virus, Phage Φ-X174; 5387 - First sequenced genomeVirus, Phage λ 5×104

Bacterium, Escherichia coli 4×106

Plant, Fritillary assyrica 13×1010 Largest known genomeFungus,Saccharomyces cerevisiae 2×107

Nematode, Caenorhabditis elegans 8×107

Insect, Drosophila melanogaster 2×108

Mammal, Homo sapiens 3×109

Note: The DNA from a single human cell has a length of ~1.8m.

Evolution

• A model/theory to explain the diversity of lifeforms

• Some aspects known, some not– An active field of research in itself

• Bioinformatics deals with genomes, which areend-products of evolution. Hence bioinformaticscannot ignore the study of evolution

“… endless forms most beautiful and most wonderful …”- Charled Darwin

Evolution

• All organisms share the genetic code• Similar genes across species• Probably had a common ancestor• Genomes are a wonderful resource to

trace back the history of life• Got to be careful though -- the

inferences may require clevertechniques

Evolution

• Lamarck, Darwin, Weissmann, Mendel

“Oh my dear, let us hopethat what Mr. Darwin says is

not true.But if it is true, let us hope

that it will not becomegenerally known!”

Theory wasn’t well-received