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

nano micro macro

DNA structure.

DNA: Deoxyribose Nucleic Acid

History:• 1868 Miescher – discovered nuclein

• 1944 Avery – experimental evidence that DNA is constituent of genes.

• 1953 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.”

• 1980 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

• 5’end 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-polymerase ribosomes

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)

• Can’t 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

– The location of direction of these periodic, repeating structures is known as the secondary structuresecondary 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 bondsbetween C=O ofresidue n, andNH of residuen+4

• 3.6 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 bitabove or below the previous

• Parallel/aniparallelParallel/aniparallel,contiguous/non-contiguous

Parallel and anti-parallel -sheets

• Anti-parallel is slightly energetically favoredAnti-parallelAnti-parallel 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)