Basic conceptsof molecular biology

Gabriella Trucco

Email: gabriella.trucco@unimi.it

What is life made of?

1665: Robert Hooke discovered that organisms are composed of individual compartments called cells

Great diversity of cells in nature, but they all have some common features

All cells have a life cycle: they are born, eat, replicate, and die

Many important decisions, but cells do not have brains complex networks of chemical reactions: pathways

More detailed discussions can be found in introductory biology textbooks like

T. Brown. Genomes. JohnWiley and Sons, New York, 2002.

B. Lewin. Genes VII. Oxford University Press, Oxford, UK, 1999.

B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J. Watson. Molecular Biology of the Cell.

Garland Publishing, New York, 1994.

The cell structure

What is life made of?

All life on this planet depends on two types of molecule:

Proteins: many different kinds: Structural proteins, enzymes, …

nucleic acids: two kinds of nucleic acids: ribonucleic acid, abbreviated by RNA, and deoxyribonucleic acid, or DNA

What is life made of?

cell’s DNA :library describing how the cell works

RNA acts to transfer certain short pieces of information to different places in the cell

Proteins form enzymes that perform biochemical reactions,

send signals to other cells,

form the body’s major components (like the keratin in our skin),

and otherwise perform the actual work of the cell.

DNA, RNA, and proteins are examples of strings written in either the four letter alphabet of DNA and RNA or the twenty-letter alphabet of proteins.

Proteins

chain of simpler molecules called amino acids

Aminoacid one central carbon atom

hydrogen atom

amino group (NH2)

carboxy group (COOH)

side chain

There are 20 common amino acids (aa’s); two systems of abbreviations are used: 3-letter-code and 1-letter-code. We usually use the 1-letter-code.

alanine Ala A

arginine Arg R

asparagine Asn N

aspartic acid Asp D

cysteine Cys C

glutamine Gln Q

glutamic acid Glu E

glycine Gly G

histidine His H

isoleucine Ile I

leucine Leu L

lysine Lys K

methionine Met M

phenylalanine Phe F

proline Pro P

serine Ser S

threonine Thr T

tryptophan Trp W

tyrosine Tyr Y

valine Val V

Proteins

Proteins Peptide bonds

Backbone

Primary, secondary, tertiary, and quaternary structures of proteins

DNA• Discovered in 1869

• Basic unit (nucleotide):

- sugar

- phosphate group

- nitrogenous base

• 4 bases (nucleotides):

- Adenine (A)

- Cytosine (C)

- Guanine (G)

- Thymine (T)

Structure of DNA

DNA: nucleotides

5’ ...AACAGTACCATGCTAGGTCAATCGA...3’

3’ ...TTGTCATGGTACGATCCAGTTAGCT...5’

orientation (read from 5’ to 3’ end)

length measured in bp (base pairs)

double stranded, the two strands are antiparallel

A - T and C - G complementary (Watson-Crick pairs)

DNA as string of letters, each letter representing a base. "string-view" of DNA: one of the strings on top of the other

Connection between DNA and proteins

Proteins could not be made directly from DNA DNA resides within the nucleus, whereas protein synthesis had been

observed to happen outside the nucleus, in the cytoplasm

mid 1950s: Paul Zamecnik discovered that protein synthesis in the cytoplasm happens with the help of certain large molecules called ribosomes that contain RNA.

DNA as a template used to copy a particular gene into messenger RNA (mRNA) that carries the gene’s genetic information to the ribosome to make a particular protein.

RNA: 4 characters A C U G: adenine, cytosine, uracil, guanine (U instead of T)

Genes

Certain contiguous stretches along DNA encode information for building proteins, but others do not

This stretch is known as a gene

Protein: chain of amino acids

Triplets of nucleotides specify each amino acid

Each nucleotide triplet is called a codon

Genetic code: table that gives the correspondence between each possible triplet and each amino acid

The genetic code

Degeneracy of the

genetic code: 64

codons but only 20

aa’s plus stop codon

Silent mutations: if

third position

mutates, this often

does not alter the aa

The central dogma of molecular biology

How the information in the DNA results in proteins

Promoter – AUG

Transcription: copy of the gene made on an RNA molecule (messenger RNA, or mRNA ). This resulting RNA will have

exactly the same sequence as one of the strands of the gene but substituting U for T

The strand identical to the mRNA is called coding strand

The other strand (the one which is used for the transcription) is called template strand

The central dogma of molecular biology

Translation: tRNA make the connection between a codon and the specific amino acid this codon codes for

Each tRNA molecule has, on one side, a conformation that has high affinity for a specific codon and, on the other side, a conformation that binds easily to the corresponding aa

As the messenger RNA passes through the ribosome, a tRNAmatching the current codon binds to it, bringing the corresponding amino acid

When a STOP codon appears, no tRNA associates with it, and the synthesis ends

Example

The transcription of DNA into RNA, and the translation of RNA into a protein

Strings in molecular biology

Many other problems in molecular biology can be modelled by strings (e.g. gene order, haplotypes, . . . )

Strings are finite sequences over an alphabet S (also called sequences)

DNA (characters: nucleotides) S = {A,C,G,T}

RNA (characters: nucleotides) S = {A,C,G,U}

Proteins (characters: peptides) S = {A,C,D,E,F,. . . ,W,Y}

Reading frames

Reading frame: one of the three possible ways of grouping bases to form codons in a DNA or RNA sequence

3 different reading frames for translation: The DNA sequence

5’ ...TATTCGAATCGGC...3’

can be translated in 3 different ways, leading to different aa sequences