Molecular Biology and Biological Chemistry The Fundamentals of Bioinformatics Chapter 1

Introduction The Scale Spectrum The Genetic Material Gene Structure and Information Content Protein Structure and Function The Nature of Chemical Bonds Molecular Biology Tools Genomic Information Content

The Scale Spectrum Nano –Genes, proteins, genetic networks Micro –Organ physiology, pharmacokinetics Macro –Whole body, multi-organism nanomicromacro

DNA structure. DNA: Deoxyribose Nucleic Acid History: 1868 Miescher – discovered nuclein 1944 Avery – experimental evidence that DNA is constituent of genes Watson&Crick – double helical nature of DNA. We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest X-ray structure of more than a full turn of DNA.

The Genetic Material Genes: –the basis of inheritance –A specific sequence of nucleotides.(nt) Nucleotide bases –4 types: Guanine(G), Adenine (A), Thymine (T), & Cytosine (C) –Only differ in their Nitrogenous base –Alphabet of the Language of Genes

Five types of bases.

Base Pairings DNA is highly redundant –Strands are complementary –Permits replication Base pairings are stable and robust –Only G-C or A-T combinations possible

Complementarity of nucleotide– bases for double stranded helical structure.

Double helical structure of DNA.

Antiparallel Nature of DNA 5end of one strand matches 3 end of other If one strand is 5-GTATCC-3 Then other is 3-CATAGG-5 Most processes go from 5 to 3, so write as: 5-GGATAC-3 Strands are reverse complements 5 is upstream, and 3 is downstream

The Genome Full complement of Genes Set of chromasomes –DNA chains

The Central Dogma DNA makes RNA makes Protein –General not universal Enzymes –Proteins that makes things happen, but are not used up –X_ase RNA-polymeraseribosomes

The Central Dogma (2) Transcription –RNA construction mediated by RNA-polymerase –One-one correspondence with DNA G, C, A, and U (Uracil) Translation –Conversion of nucleotides to amino acids –Ribosomes - complex structure of RNA & protein –Mediates protein synthesis

The Central Dogma (3)

Gene Structure and Information Content Information formatting and interpretation is very important –Alphabet and punctuation Same language used for both: –Prokaryotes (bacteria) –Eukaryotes (more complex life forms)

Promoter Sequences Gene Expression –Process of using information in DNA to make RNA molecule then a corresponding protein Expressing right quantity of protein essential for survival Two crucial distinctions –Which part of genome is start of a gene –Which genes code for proteins needed at a particular time Responsibility falls to RNA-polymerase

Promoter sequences (2) Cant look for single nucleotide –1 in 4 chance of appearing at random –General probability of a sequence = (1/4) n Prokaryotes: 13 nt promoter sequences –1 in 70 million chance of random appearance –Genome a few million nts long –Datum: 1nt, 6 that are 10 nts upstream & 6 that are 35 nts upstream Eukaryotes are several orders of magnitude bigger

Promoter Sequences (3) Two types of Genes: 1.Structural Cell structure or metabolism 2.Regulatory Production control Positive regulation Negative regulation

The Genetic Code Need way to robustly translate from DNA to Protein –4 nt alphabet –20 amino acid (aa) alphabet –Mismatch Codon (triplet code) –1&2 nts give < 20 –Each aa coded by a codon –Degeneracy: more than 1 codon per aa = robustness –Stop codon: full stop

The Genetic Code

Open Reading Frames (ORFs) Start codon: AUG (and methinine) Reading frame –Established by start codon –Necessary for accurate translation –Mistakes lead to wrong proteins (& premature stops) Open Reading Frame –Inordinately long reading frame with no stop codon –Proteins 100s of aa long –Random stop: 1 in 20 –Distinguishing feature of prokaryotes and eukaryotes.

Introns and Exons Messenger RNA - perfect copy of DNA Introns: locally uninformative sequences in mRNA Exons: locally informative sequences in mRNA Splicing: removal of introns, rejoining exons Spliceosomes: enzymes that do splicing –GT-AG rule (potentially too common) –Checks 6 extra nts –Allows subtle nuances

Introns and Exons (2)

Protein Structure and Function Proteins are molecular machinery that performs most work in cells Vast array of tasks –Structure, catalysis, transportation, signalling metabolism … Highly complex compounds –Primary, secondary, tertiary, quaternary structure.

Primary & Secondary Structure Primary structurePrimary structure = the linear sequence of amino acids comprising a protein: AGVGTVPMTAYGNDIQYYGQVT… Secondary structureSecondary structure –Regular patterns of hydrogen bonding in proteins result in two patterns that emerge in nearly every protein structure known: the -helix and the -sheet secondary structure –The location of direction of these periodic, repeating structures is known as the secondary structure of the protein

Planarity of the peptide bond Phi ( ) – the angle of rotation about the N-C bond. Psi ( ) – the angle of rotation about the C -C bond. The planar bond angles and bond lengths are fixed.

Phi and psi = = 180° is extended conformation : C to N–H : C=O to C C C=O N–H

The alpha helix 60°

Properties of the alpha helix 60° Hydrogen bondsHydrogen bonds between C=O of residue n, and NH of residue n residues/turn 1.5 Å/residue rise 100°/residue turn

The beta strand (& sheet) 135° +135°

Properties of beta sheets Formed of stretches of 5-10 residues in extended conformation Pleated – each C a bit above or below the previous Parallel/aniparallelParallel/aniparallel, contiguous/non-contiguous

Parallel and anti-parallel -sheets Anti-parallel is slightly energetically favored Anti-parallelParallel

Molecular Biology Tools Restriction enzyme digests Gel electrophoresis Blotting and hybridization Cloning Polymerase chain reaction DNA sequencing

Genomic Information Content C-value paradox –No correlation between organism complexity and DNA size Reassociation Kinetics –Denaturing/renaturing –Cot equation: t0.5 –Junk DNA

… & Finally There are only 10 types of people in the world: those that understand binary and those that do not Pete Smith (or Anon)