BASIC MOLECULAR BIOLOGY

(Borrowed from “An Introduction to Bioinformatics Algorithms” by Neil C. Jones and Pavel A. Pevzner and further modified by Prof. Natalio Krasnogor)

Outline For Section 1:

• All living things are made of Cells – Prokaryote, Eukaryote

• Cell Signaling• What is Inside the cell: From DNA, to RNA, to

Proteins

Cells

• Fundamental working units of every living system. • Every organism is composed of one of two radically different types of cells: prokaryotic cells or eukaryotic cells.• Prokaryotes and Eukaryotes are descended from the same primitive cell.

– All extant prokaryotic and eukaryotic cells are the result of a total of 3.5 billion years of evolution by natural selection.

Hard Fact! No pre-medieval fairy tales like ID, Adam&Eve,

etc

For more information:“The Major Transitions in

Evolution” by M. Smith and E. Szathmary

Cells

• Chemical composition-by weight – 70% water– 7% small molecules

• salts• Lipids• amino acids• nucleotides

– 23% macromolecules• Proteins• Polysaccharides• lipids

Life begins with Cell

• A cell is the smallest structural unit of an organism that is capable of sustained independent functioning

• All cells have some common features• What is Life? Can we create it in the lab? Read:The imitation game—a computational chemical approach to recognizing life.

Nature Biotechnology, 24:1203-1206, 2006

2 types of cells: Prokaryotes & Eukaryotes

All Cells have common Cycles

• Born, eat, replicate, and die

Prokaryotes and Eukaryotes

•According to the most recent evidence, there are three main branches to the tree of life. •Prokaryotes include Archaea (“ancient ones”) and bacteria.•Eukaryotes are kingdom Eukarya and includes plants, animals, fungi and certain algae.

Prokaryotes and Eukaryotes, continued

Prokaryotes Eukaryotes

Single cell Single or multi cell

No nucleus Nucleus

No organelles Organelles

One piece of circular DNA (plasmid)

Chromosomes

No mRNA post transcriptional modification

Exons/Introns splicing

Prokaryotes v.s. EukaryotesStructural differences

Prokaryotes Eubacterial (blue green algae) and archaebacteria only one type of membrane-- plasma membrane forms

the boundary of the cell proper The smallest cells known are

bacteria Ecoli cell 3x106 protein molecules 1000-2000 polypeptide species.

Eukaryotes plants, animals, Protista, and fungi

complex systems of internal membranes forms organelle and compartments

The volume of the cell is several hundred times larger Hela cell 5x109 protein molecules 5000-10,000 polypeptide species

Signaling Pathways: Control Gene Activity

• Instead of having brains, cells make decisions through complex networks of chemical reactions, called pathways– Synthesize new materials– Break other materials down for spare parts– Signal to eat, die, reproduce, sporulate, etc

• Even Bacteria are smart entities. Read:Bacteria Harnessing Complexity by E. Ben-

Jacob and colleagues

Example of cell signaling

Cells Information and Machinery• Cells store all information to replicate itself

– Human genome is around 3 billions base pairs long– Almost every cell in human body contains same set of

genes– But not all genes are used or expressed by those cells

• Machinery:– Collect and manufacture components– Carry out replication– Kick-start its new offspring

(A cell is like a car factory but FAR more complex and efficient)

Overview of organizations of life

• Nucleus = library• Chromosomes = bookshelves• Genes = books• Almost every cell in an organism contains the same

libraries and the same sets of books.• Books represent all the information (DNA) that every

cell in the body needs so it can grow and carry out its various functions.

• Moreover, more recent discoveries suggest that the books, bookshelves and libraries are not passive waiting to be read but are, sometimes, rewriting and rewiring themselves!

Terminology

• The genome is an organism’s complete set of DNA.– a bacteria contains about 600,000 DNA base pairs– human and mouse genomes have some 3 billion.

• human genome has 23 distinct chromosomes.– Each chromosome contains many genes.

• Gene – basic physical and functional units of heredity. – specific sequences of DNA bases that encode

instructions on how and when to make proteins. • Proteins

– Make up the cellular structure– large, complex molecules made up of smaller subunits

called amino acids.

All Life depends on 3 critical molecules

• DNAs– Hold information on how cell works

• RNAs– Act to transfer short pieces of information to different parts of cell– Provide templates to synthesize into protein

• Proteins– Form enzymes that send signals to other cells and regulate gene

activity– Form body’s major components (e.g. hair, skin, etc.)– Are life’s laborers!

• Computationally, all three can be represented as sequences of a certain 4-letter (DNA/RNA) or 20-letter (Proteins) alphabet

DNA, RNA, and the Flow of Information

TranslationTranscription

Replication

Weismann Barrier / Central Dogma ofMolecular Biology

Overview of DNA to RNA to Protein

• A gene is expressed in two steps1) Transcription: RNA synthesis2) Translation: Protein synthesis

DNA: The Basis of Life• Deoxyribonucleic Acid (DNA)

– Double stranded with complementary strands A-T, C-G

• DNA is a polymer– Sugar-Phosphate-Base– Bases held together by H bonding to the opposite strand

RNA• RNA is similar to DNA chemically. It is usually

only a single strand. T(hyamine) is replaced by U(racil)

• Some forms of RNA can form secondary structures by“pairing up” with itself. This can have impact on its properties dramatically.

DNA and RNA

can pair with

each other.http://www.cgl.ucsf.edu/home/glasfeld/tutorial/trna/trna.giftRNA linear and 3D

view:

RNA, continuedSeveral types exist, classified by function:

• hnRNA (heterogeneous nuclear RNA): Eukaryotic mRNA primary transcipts with introns that have not yet been excised (pre-mRNA).

• mRNA: this is what is usually being referred to when a Bioinformatician says “RNA”. This is used to carry a gene’s message out of the nucleus.

• tRNA: transfers genetic information from mRNA to an amino acid sequence as to build a protein

• rRNA: ribosomal RNA. Part of the ribosome which is involved in translation.

Transcription• Transcription is highly regulated. Most DNA is in a

dense form where it cannot be transcribed. • To start, transcription requires a promoter, a small

specific sequence of DNA to which polymerase can bind (~40 base pairs “upstream” of gene)

• Finding these promoter regions is only a partially solved problem that is related to motif finding.

• There can also be repressors and inhibitors acting in various ways to stop transcription. This makes regulation of gene transcription complex to understand.

Definition of a Gene

• Regulatory regions: up to 50 kb upstream of +1 site

• Exons: protein coding and untranslated regions (UTR)1 to 178 exons per gene (mean 8.8)8 bp to 17 kb per exon (mean 145 bp)

• Introns: splice acceptor and donor sites, junk DNAaverage 1 kb – 50 kb per intron

• Gene size: Largest – 2.4 Mb (Dystrophin). Mean – 27 kb.

Splicing

Splicing and other RNA processing

• In Eukaryotic cells, RNA is processed between transcription and translation.

• This complicates the relationship between a DNA gene and the protein it codes for.

• Sometimes alternate RNA processing can lead to an alternate protein (splice variants) as a result. This is true in the immune system.

Proteins: Crucial molecules for the functioning of life

• Structural Proteins: the organism's basic building blocks, eg. collagen, nails, hair, etc. • Enzymes: biological engines which mediate multitude of biochemical reactions. Usually enzymes are very specific and catalyze only a single type of reaction, but they can play a role in more than one pathway. • Transmembrane proteins: they are the cell’s housekeepers, eg. By regulating cell volume, extraction and concentration of small molecules from the extracellular environment and generation of ionic gradients essential for muscle and nerve cell function (sodium/potasium pump is an example)

• Proteins are polypeptide chains, constructed by joining a certain kind of peptides, amino acids, in a linear way• The chain of amino acids, however folds to create very complex 3D structures

Translation

• The process of going from RNA to polypeptide.

• Three base pairs of RNA (called a codon) correspond to one amino acid based on a fixed table.

• Always starts with Methionine and ends with a stop codon

Amino Acids

Protein Structure: Introduction

• Different amino acids have different properties

• These properties will affect the protein structure and function

• Hydrophobicity, for instance, is the main driving force (but not the only one) of the folding process

Protein Structure: Hierarchical nature of protein structure

MKYNNHDKIRDFIIIEAYMFRFKKKVKPEVDMTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFDQIIKQFNLADQSESQMIPKDSKEFLNLMMYTMYFKNIIKKHLTLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLLAQVNQLLADKDHLHLVFE

Primary Structure = Sequence of amino acids

Secondary Structure Tertiary

Local Interactions Global Interactions

Protein Structure: Why is structure important?

The function of a protein depends greatly on its structure

The structure that a protein adopts is vital to it’s chemistry

Its structure determines which of its amino acids are exposed to carry out the protein’s function

Its structure also determines what substrates it can react with

Protein Structure: Mostly lacking information

• Therefore, it is clear that knowing the structure of a protein is crucial for many tasks

• However, we only know the structure for a very small fraction of all the proteins that we are aware of– The UniProtKB/TrEMBL archive contains 23165610 (16886838)

sequences– The PDB archive of protein structure contains only 84223(76669)

structures• In the native state, proteins fold on its own as soon as

they are generated, amino-acid by amino-acid (with few exceptions e.g. chaperones) can we predict this process as to close the gap between protein sequences and their 3D structures?

Central Dogma of Biology: A Bioinformatics Perspective

The information for making proteins is stored in DNA. There is a process (transcription and translation) by which DNA is converted to protein. By understanding this process and how it is regulated we can make predictions and models of cells.

Sequence analysis

Gene Finding

Protein Sequence/Structure Analysis

Assembly

Computational Problems