Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Basic Biology

Gina Cannarozzi

28th October 2005

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Class Overview

DNA RNA ProteinGenomics Transcriptomics Proteomics

Genome wide Genome Comparison Microarrays Orthology: Familiescomparison and Sequencing of Proteins

Transcription factorGene Finding binding sites

Single sequence Molecular Evolution Secondary Structureand Family Experimental Predictioncomparison Techniques Molecular Evolution

Tools:I String AlignmentI Phylogenetic Tree ConstructionI Multiple Sequence Al

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Outline

1. biological macromolecules - proteins and DNA/RNA

2. interaction of proteins, DNA and RNA is described bythe Central Dogma of Molecular Biology - DNA isorganized into genes, the genes are transcribed toRNA and translated to proteins

3. DNA, RNA

4. proteins

5. molecular evolution - continual process of randommutation and natural selction

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Central Dogma

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Vocabulary

Genome - The entire set of hereditary instructions for building,running and maintaining an organism. The genomeencompasses the material passed on from generation togeneration. (does not vary within one organism)Genomics - study of the structure and function of the genomeTranscriptome - The entire set of messenger RNA expressedwhile building, running and maintaining an organism. Thetranscriptome is all the mRNA transcribed from genes within agiven genome. (varies depending on physiology)Transcriptomics - The genome-wide study of mRNA expressionlevels.Proteome - The entire set of proteins expressed while building,running and maintaining an organism. The proteome is all theprotein translated from mRNA of a given transcriptome. (varieswith physiology)Proteomics - study of the structure and function of theproteome

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Biology

I Biology = Science of living thingsI What is Life?

- As a rule: living organisms exchange matter andenergy with their environment, grow, develop,die, react to their environment and reproduce

- Exceptions: seeds in vegetative state, viruses,viroids, prions...

- VirusesI have DNA or RNA (genetic material)I evolveI can not use the genetic material themselves, they

must have a host cell to function and reproduceI does not use enery themselves but the cells they

infect do use energyI are they alive?

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Computational Biology

I truely interdisciplinaryI biology is described by general rules with many

many exceptionsI computer science is more clearly definedI probability and statistics is important to describe

general rules with many exceptionsI input data can be flawed

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Composition of Organisms

I All organisms are based on similar biochemicalprocesses.

I Main actors in these processes:→ Proteins→ Nucleic Acids (DNA/RNA)

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

DNA Vocabularynucleotide or nucleic acid or base one unit of DNAcomprised of a base, a sugar and and a phosphate groupoligonucleotide polymer of more than 1 nucleic acidpurine bases adenine and guaninepyrimidine bases thymine and cytosinetransition conversion between a purine and a purine or apyrimidine and a pyrimidinetransversion conversion between a purine and apyrimidinecodon 3 bases that code for 1 amino acidreading frame one of 3 possible ways to read a nucleotidesequences in one directionframeshift type of mutation in which an insertion ordeletion changes the reading frameintrons part of a gene that is transcribed but not presentin a mature mRNA after splicingexons part of a gene that is present in the mature mRNAand is translated to proteinmRNA messenger RNA; arises in the process oftranscription from the DNA and includes information onthe synthesis of a proteintRNA transfer RNA; a set of RNAs that act during proteinsynthesis matching individual amino acids to theircorresponding codon on a mRNA

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Nucleic Acids

I Proteins are synthesized from information encodedin genes in DNA.

→ Nucleic Acids (NA)I 2 types of NA:

1. Deoxiribonucleic acid (DNA)2. Ribonucleic acid (RNA)

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

DNA

I DNA consists of 2 strandsI Each strand has 3 components:

1. Phosphate residue2. Sugar: 2’-deoxyribose3. 4 bases: Adenine (A), Cytosine (C), Guanine (G),

Thymine (T)

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Bases in DNA

pyrimidines Cytosine, Thymine purines Adenine, Guanine

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

DNA

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

RNA

The same as DNA except the sugar is ribose and thebase Uracil (U) replaces Thymine (T).:

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

RNA II

I single stranded → folds on to itself

→ can take many different configurationsI has many different functions. 2 most important:

1. mRNA: messenger RNA, information transport2. tRNA: transfer RNA3. rRNA: ribosomal RNA4. ribozymes: RNA with enzymatic functions

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

DNA Repair Mechanisms

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Take Home Message: DNA/RNA

I DNA/RNA - strands have a repetitive pattern:

−[Sugar − Phosphate]−

→ chain structureI Orientation: 5′ → 3′

I small number of bases and double strandedness ofDNA insures secure data storage

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Take Home Message: DNA/RNA II

Definition of alphabets:

ADNA := {A, C, G, T} ARNA := {A, C, G, U}

DNA sequence:

sDNA = B1 · B2 · ... · Bn =n∏

i=1

Bi where ∀ni=1Bi ∈ ADNA

RNA sequence:

sRNA = B1 · B2 · ... · Bn =n∏

i=1

Bi where ∀ni=1Bi ∈ ARNA

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Proteins

I Main component of all organismsI Peform most functions in the Cell

1. Structural proteins: e.g. muscle filaments in a body2. Enzymes: catalysts for chemical reactions. Speed

up of reaction and decrease in energy requirement.3. Signalling Proteins: e.g. cell receptors for estrogen)

I Proteins are built of simpler building blocks called:

→ Amino Acids (AA)

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Amino Acids

Common structure of Amino Acids:

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Amino Acids II

I In nature, 20 amino acids are commonI Amino acids differ in their side chains (R)I Side chains can be as simple as a hydrogen atom or

as complex as two carbon rings.I Characteristics of side change that can influence

their chemistry are: hydrophobicity, charge, acidity,basicity, and size

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Amino Acids II

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Alle mini hydrophiles by Gina Cannarozzi

Alle mini hydrophilesKREND, KRENDFAMILYVW are hydrophobes.They dont like the sea.

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

"My name is Bond, Peptide Bond"

Question: How do amino acids form proteins? [→]

Peptide bonds

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Central Dogma of Molecular Biology

The central dogma of biology states that the coded geneticinformation hard-wired into DNA is transcribed into individualtransportable cassettes, composed of messenger RNA (mRNA); eachmRNA cassette contains the program for synthesis of a particularprotein (or small number of proteins).

Sources: Definition from Chapter 1: The Dynamic Cell, of Molecular

Cell Biology. Illustration adapted from the National Human Genome

Research Institute (NHGRI) Genetic Illustrations entry for mRNA.

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Transcription

DNA

precursorRNA

Exon1 Intron 1 Exon 2

Exon1 Exon 2

copy

Intron 2 Exon 3

Exon 3

splicing

mRNA

transport to ribosome

Stop

Research questions:

Where are the introns? Where are the coding sequences? Where are

the stop and start of translation? Where are the transcription factors

that control when transcription takes place?

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Translation

How is a mRNA sequence mapped to a protein?

→ The genetic codeI Groups of 3 subsequent bases are translated into 1

amino acid

→ Codons

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

The Genetic Code

GGG G Gly AGG R Arg CGG R Arg UGG W TrpGGA G Gly AGA R Arg CGA R Arg UGA StopGGC G Gly AGC S Ser CGC R Arg UGC C CysGGU G Gly AGU S Ser CGU R Arg UGU C Cys

GAG E Glu AAG K Lys CAG Q Gln UAG StopGAA E Glu AAA K Lys CAA Q Gln UAA StopGAC D Asp AAC N Asn CAC H His UAC Y TyrGAU D Asp AAU N Asn CAU H His UAU Y Tyr

GCG A Ala ACG T Thr CCG P Pro UCG S SerGCA A Ala ACA T Thr CCA P Pro UCA S SerGCC A Ala ACC T Thr CCC P Pro UCC S SerGCU A Ala ACU T Thr CCU P Pro UCU S Ser

GUG V Val AUG M Met CUG L Leu UUG L LeuGUA V Val AUA I Ile CUA L Leu UUA L LeuGUC V Val AUC I Ile CUC L Leu UUC F PheGUU V Val AUU I Ile CUU L Leu UUU F Phe

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Translation in the Ribosome

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Formal representation of proteins

I Each amino acid represented by one letter

→ all amino acids as alphabet:

A := {A, R, N, D, C, Q, E , G, H, I, L, K , M, F , P, S, T , W , Y , V}

I Together with chain structure and orientation

→ proteins can be represented as strings

p = a1 · a2 · ... · an =n∏

i=1

ai where ∀ni=1ai ∈ A

where “·” denotes the concatenation operator (Diss Knecht,1996)

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Protein Structures

I From a biological point of view proteins are not juststrings

I Proteins fold into 3D-configurationsI each amino acid can behave differently depending

on the situationI Characterization of proteins with the following

structures:I Primary: sequenceI Secondary: alpha helix or beta strand which arrange

into sheetsI Tertiary: packing of secondary structuresI Quaternary: higher order packing

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Primary Structure

I the sequence of 20 amino acidsKLKDYKHAYHPVDLDIKDIDYTMFHLACITKLFDGD...

I linear (unbranched)I Repetitive motive of: [−N − C − (CO)−]→ backbone → chain structure

I Orientation from N− to C− terminal endI 50-3000 amino acids

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Secondary Structure- alpha Helix (H)I alpha helices have 3.6 residues per turn. (100

degrees separate the side chains of consecutiveresidues)

I there is a hydrogen bond between residue i andresidue i+4

I average length of an alpha helix is 11 amino acidsalthough they can be as short as 5 and as long as 25

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Secondary Structure- beta strands

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Tertiary Structure- the "fold" of the protein

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Summary

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

crystal structure of Triose PhosphateIsomerase

Dimer (two identical proteins together) with beta-barrelfold.

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Protein Vocabulary

amino acid or residue building blocks of proteinsbackbone the N-C-C -N-C-C bonds that form the chain of the proteinside chains the part of each amino acid that gives the distinctivecharacteristic and carries the functionality (acidic, basic, charged + or-, hydrophobic, hydrophilic)fold refers to the 3 dimensional structure - common folds are, forexample, a barrel or an alpha/beta sandwichhydrophobicity characteristic of amino acid side chains thatdetermines much of how they behave- are they compatible with wateror not?hydrophobic do not like water (FAMILYVW)hydrophilic like water (KREND)hydrogen bonding a strong type of intermolecular attraction based onpartial charges. Occurs between hydrogen and F, O and N.alpha helix a helix formed in a protein (not the same as double helix ofDNA)- characterized by hydrogen bonds between residue i and i+4

beta strand an extended chain conformation in a protein in which the

side chains stick out on alternating sides and hydrogen bonding is

between neighboring strands in sheets. Beta strands are almost

always arranged into sheets.

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Molecular Evolution

I Over time DNA sequences change due to→ UV-radiation, Toxins, Radioactivity, other factors ...

I ... as a consequence, DNA undergoes→ Mutations: Change of one base to another base→ Deletions of bases→ Insertions of bases

I Other evolutionary forces

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Evolution, Phylogeny and the Alignment

Rice Corn Dog Fly Mosquito

||....!..!.|!|..|.!.:. .||||. | .!|.:.~|||NGTTD!VDKIVKILNEGQIASTDVVEVVVSPPYVFLPVVKSQL

NGDKASIADLCKVLTTGPLNAD−−TEVVVGCPAPYLTLARSQL

Rice

Mosquito

I alignment implies an evolutionary relationship represented byPhylogenetic Tree

I alignmnet shows accepted substitutions since divergenceI our model allows for point mutations and insertions/deletions

(indels)I aligns amino acids that diverged from the same residue in

(hypothetical) most recent common ancestorI darwinian evolution is driven by mutation and natural selectionI mutations may be adaptive, neutral or deleteriousI proteins evolve under functional constraints - mutations that

destroy function do not appear in database via organism deathI "correct" alignment represents actual events- substitutions,

indelsI impossible to verify -> take alignment with the highest probability

that the alignment is correct under our model

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Tree of Life

tree courtesy of Daniel Margadant

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Molecular Evolution Vocabulary

homology related by common ancestryhomologs biological sequences related by commonancestryorthology homology that arises via speciationparalogy homology that arises via gene duplicationeukaryote one of the 3 kingdoms of life, organisms thathave a nucleusprokaryote organisms that lack a nucleusarchaea one of the 3 kingdoms of life, prokaryotes thatoften live in extreme environments (hot, salty, cold, basic,acidic)bacteria one of the 3 kingdoms of life, prokaryotes

Basic Biology

Gina

Introduction

DNA

Proteins

Central Dogma

Protein Structure

MolecularEvolution

Web Sites

I Course:http://www.icos.ethz.ch/education/courses/computational_biology

I CBRG:http://www.cbrg.ethz.ch/

I BioRecipes:http://www.biorecipes.com