Information Storage and Processing in Biological Systems: A seminar - - PowerPoint PPT Presentation

Information Storage and Processing in Biological Systems: A seminar course for the Natural Sciences

• Sept. 11

Biological Information, Sept 16 DNA, Gene regulation

Sept 18 Translation and Proteins

Sept 23 Enzymes and Signal transduction Sept 25 Biochemical Networks Sept 30 Simple Genetic Networks (Dr. Jacob) Oct 2

Background ÿ The Thread of Life. Susan Aldridge. Chapter 2 ÿ Molecular Biology of the Cell. Alberts et al. Garland Press Suggested further reading

• Protein molecules as computational elements in living cells. D. Bray.
• Nature. 1995 Jul 27;376(6538):307-12.
• Signaling complexes: biophysical constraints on intracellular
• communication. D. Bray. Annu Rev Biophys Biomol Struct. 1998;27:59-75.
• Metabolic modeling of microbial strains in silico. Ms W. Covert, et al.

Trends in Biochemical Sciences Vol.26 ( 2001). 179-186.

• Modelling cellular behaviour. D. Endy & R. Brent. Nature(2001) 409: 391-

395.

A - Introduction to Proteins / Translation

• The primary structure is defined as the sequence of amino acids in the
• protein. This is determined by and is co-linear to the sequence of bases

(triplet codons) in the gene*. 5’---CTCAGCGTTACCAT---3’ 3’---GAGTCGCAATGGTA---5’ 5’---CUCAGCGUUACCAU---3’ N---Leu-Ser-Val-Thr---C DNA RNA PROTEIN

transcription translation

* - this is not strictly true in most eukaryotic genomes

Structure of Genes In Eukaryotic Organisms

hnRNA

heterogeneous nuclear RNA

RNA splicing Transcription mRNA

hnRNA

heterogeneous nuclear RNA

RNA splicing Transcription mRNA

Introns Structure of Genes In Eukaryotic Organisms Exons

Structure of Genes In Eukaryotic Organisms

hnRNA

heterogeneous nuclear RNA

RNA splicing Transcription mRNA mRNA Alternative RNA splicing

Structure of Genes In Eukaryotic Organisms

hnRNA

heterogeneous nuclear RNA

RNA splicing Transcription mRNA Control Elements

Structure of Genes In Eukaryotic Organisms

• Coding sequence can be discontinuous and the gene can be composed of

many introns and exons.

• The control regions (= operators) can be spread over a large region of

DNA and exert action-at-a-distance.

• There can be many different regulators acting on a single gene – i.e. more

signal integration than in bacteria.

• Alternate splicing can give rise to more than one protein product from a

single ‘gene’.

• Predicting genes (introns, exons and proper splicing) is very challenging.
• Because the control elements can be spread over a large segment of DNA,

predicting the important sites and their effects on gene expression are not very feasible at this time.

Translation

Note that many ribosomes can read one message like beads on a string generating many polypeptide chains simultaneously.

• Translation is the synthesis of a polypeptide (protein) chain using the mRNA

template.

• Note the mRNA has directionality and is read from the 5’end towards the 3’end.

Translation

• The 5’end is defined at the DNA level by the promoter but this does not define

the translation start.

• The translation start sets the ‘register’ or reading frame for the message.
• The end is determined by the presence of a STOP codon (in the correct reading

frame).

Schematic Illustration of Translation

Protein Synthesis involves specialized RNA molecules called transfer RNA

• r tRNA.

The translation start is dependent on: 1) a sequence motif called a ribosome binding site (rbs) 2) an AUG start codon 5-10 bp downstream from the rbs

Translation Start Position

3’end of 16S rRNA 3’AU //-5’ UCCUCA |||||| 5’-NNNNNNNAGGAGU-N5-10-AUG-//-3’ mRNA rbs start

In bacteria a single mRNA molecule can code for several proteins. Such messages are said to be polycistronic. Since the message for all genes in such a transcript are present at the same concentration (they are on the same molecule), one might predict that translation levels will be the same for all the

• genes. This is not the case: translation efficiency can vary for the different

messages within a transcript. Gene 1 Gene 2 Gene 3 Gene 4

Promoter (Start) Terminator (Stop) mRNA DNA

4 genes , 1 message

Polycistronic mRNA

Tar Tap R B Y Z

5000 1000 <100 1000 18000 10000

(Protein monomer per cell)

Translation Efficiency is an important part of gene expression

A single mRNA may encode several proteins. The final level of each protein may vary significantly and is a function of: 1) translation efficiency 2) protein stability

Translation

B – Introduction to Proteins / Characteristics

• The primary structure is defined as the sequence of amino acids in the
• protein. This is determined by and is co-linear to the sequence of bases

(triplet codons) in the gene*. 5’---CTCAGCGTTACCAT---3’ 3’---GAGTCGCAATGGTA---5’ 5’---CUCAGCGUUACCAU---3’ N---Leu-Ser-Val-Thr---C DNA RNA PROTEIN

transcription translation

* - this is not strictly true in most eukaryotic genomes

H2NCHCCH3OHO

amino group carboxylic acid amino acid (alanine)

There are 20 naturally occurring amino acids in proteins, each with distinctive ‘side chains’ that give them characteristic chemical properties.

H2NCHCCH3OHO

amino group carboxylic acid amino acid (alanine)

There are 20 naturally occurring amino acids in proteins, each with distinctive ‘side chains’ that give them characteristic chemical properties.

a-carbon

Amino acids differ in the side chains on the a-carbon.

H2NCHCCH3OHO

amino group carboxylic acid amino acid (alanine)

There are 20 naturally occurring amino acids in proteins, each with distinctive ‘side chains’ that give them characteristic chemical properties.

a-carbon

Amino acids differ in the side chains on the a-carbon.

• CH3 (methyl)

H2NCHCCH2OHOHN H2NCHCCH3OHO CHCCH2OHOHNH2NCHCCH3HNO

H2O

+

peptide bond

Alanine + Tyrptophan

(ala) + (trp) (A) + (W)

Dipeptide

(Ala-Trp) By convention polypeptides are written from the N-terminus (amino) to the C-terminus (carboxy)

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

H2NCHCHOHO HNCOHO

H2NCHCCH2OHOSH

Glycine Proline Cysteine

The Newly Synthesized Polypeptide

• The information from DNA‡RNA‡Protein is linear and the final

polypeptide synthesized will have a sequence of amino acids defined by the sequence of codons in the message.

• The sequence of amino acids is called the primary structure.
• Secondary structure refers to local regular/repeating structural elements.
• The folded three dimensional structure is referred to as tertiary structure.

Protein function depends on an ordered / defined three dimensional folding. The final three dimensional folded state of the protein is an intrinsic property of the primary sequence. How the primary sequence defines the final folded conformation is generally referred to as the Protein Folding Problem.

Primary structure of green fluorescent protein (single letter AA codes)

SEQUENCE 238AA 26886MW

MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKL PVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNY KTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKN GIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNE KRDHMVLLEFVTAAGITHGMDELYK

The primary sequence can be derived directly from the gene sequence but going from sequence to structure or sequence to function is not possible unless there is a related protein for which structure or function is known. Likewise, the structure alone rarely provides information about function (only if the function of a related protein is known).

Projections of the Tertiary Structure of Green Fluorescent Protein

Backbone tracing

Projections of the Tertiary Structure of Green Fluorescent Protein

Backbone tracing Ile188-Gly189-Asp190-Gly191-Pro192-Val193

Projections of the Tertiary Structure of Green Fluorescent Protein

“Ribbon diagram” showing secondary structures

Projections of the Tertiary Structure of Green Fluorescent Protein

“Ribbon diagram” showing secondary structures Secondary structures a-helix

Projections of the Tertiary Structure of Green Fluorescent Protein

“Ribbon diagram” showing secondary structures Secondary structures a-helix b-strand

Projections of the Tertiary Structure of Green Fluorescent Protein

“Wireframe” model showing all atoms and chemical bonds. Ile188-Gly189-Asp190-Gly191-Pro192-Val193

Projections of the Tertiary Structure of Green Fluorescent Protein

“Stick” model showing all atoms and chemical bonds. “Space filling” model where each atom is represented as a sphere of its Van der Waals radius.

MSKGEELFTGVVPILV ELDGDVNGHKFSVSG EGEGDATYGKLTLKFI CTTGKLPVPWPTLVTT FSYGVQCFSRYPDHM KQHDFFKSAMPEGYV QERTIFFKDDGNYKTR AEVKFEGDTLVNRIEL KGIDFKEDGNILGHKL EYNYNSHNVYIMADK QKNGIKVNFKIRHNIE DGSVQLADHYQQNTP IGDGPVLLPDNHYLST QSALSKDPNEKRDHM VLLEFVTAAGITHGM DELY

Random Coil “Denatured” “Unfolded” “Native” “Folded”

“folding” “denaturation”

The final folded three dimensional (tertiary) structure is an intrinsic property of the primary structure.

Primary structure Tertiary Structure

In general, proteins are unstable outside of the cell and very sensitive for solvent conditions.

Active site - the region of a protein (enzyme) to which a substrate molecule binds.

• The active site is formed by the three dimensional folding of the peptide

backbone and amino acid side chains. (lock and key / induced fit)

• The active site is highly specific in binding interactions (stereochemical

specificity). The three dimensional structure of CAP and the cAMP ligand-binding site

(Figures 3-45 and 3-55 from Alberts)

Proteins can undergo changes in their three dimensional structure in response to changing conditions or interactions with other molecules. This usually alters the ‘activity’ of the protein.

Conformational Change in Protein Structure

Proteins can undergo changes in their three dimensional structure in response to changing conditions or interactions with other molecules. This usually alters the ‘activity’ of the protein.

Conformational Change in Protein Structure

Binding of the substrate (glucose) cause the protein (hexokinase) to shift from an open to closed conformation. (Fig. 5-2, Alberts)