Biological background: Molecular Biology

Class web site:

http://statwww.epfl.ch/davison/teaching/Microarrays/ETHZ/

Statistics for Microarrays

Two types of organisms*

* Every biological ‘rule’ has exceptions!

http://www.stg.brown.edu/webs/MendelWeb/MWtoc.html

Mendelian Genetics

Human Chromosomes

Human Chromosome Banding Patterns

Chromosomes and DNA

Mitosis and Meiosis Compared

Nature (1953), 171:737

“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.”

DNA Structure Discovery

DNA• A deoxyribonucleic acid or DNA molecule

is a double-stranded linear polymer composed of four molecular subunits called nucleotides

• Each nucleotide comprises a phosphate group, a deoxyribose sugar, and one of four nitrogen bases: adenine (A), guanine (G), cytosine (C), or thymine (T)

• The two strands are held together by weak hydrogen bonds between complementary bases

• Base-pairing occurs according to the rule: G pairs with C, and A pairs with T

DNA A-type (140D)(low water content)

DNA B-type (7BNA)(Watson-Crick form)

DNA Z-type (2ZNA)(high salt concentration)

Polymorphic DNA Tertiary Structures

Genes are linearly arranged along chromosomes

DNA Structure (overview)

A nucleotide is a phospate, a sugar, and a purine (A, G) or a pyramidine (T, C) base.

The monomeric units of nucleic acids are called nucleotides.

DNA Structure

Proteins

• Proteins: macromolecules composed of one or more chains of amino acids

• Amino acids: class of 20 different organic compounds containing a basic amino group (-NH2) and an acidic carboxyl group (-COOH)

• The order of amino acids is determined by the base sequence of nucleotides in the gene coding for the protein

• Proteins function as enzymes, antibodies, structures, etc.

Amino acid codes

AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTrpTyrVa lAsxGlxSecUnk

ARNDCQEGHILKMFPSTWYVBZUX

AlanineArginineAsparagineAspartic acidCysteineGlutamineGlutamic acidGlycineHistidineIsoleucineLeucineLysineMethioninePhenylalanineProlineSerineThreonineTryptophanTyrosineVa lineAsn or AspGln or GluSelenocysteineUnknown

Primary Protein Structure

Multiple Levels of Protein Strucure

( Protein folding)

Tertiary Structure ofSperm whale myoglobin (1MBN)

(RT)

Nature (1953), 171:737

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

DNA Replication

DNA Replication

• The DNA strand that is copied to form a new strand is called a template

• In the replication of a double-stranded or duplex DNA molecule, both original (parental) DNA strands are copied

• When copying is finished, the two new duplexes, each consisting of one of the original strands plus its copy, separate from each other (semiconservative replication)

Semiconservative Replication

DNA Replication, ctd• Synthesis occurs in the chemical direction 5’3’• Nucleic acid chains are assembled from 5’

triphosphates of deoxyribonucleosides (the triphosphates supply energy)

• DNA polymerases are enzymes that copy DNA• DNA polymerases require a short preexisting DNA

strand (primer) to begin chain growth. With a primer base-paired to the template strand, a DNA polymerase adds nucleotides to the free hydroxyl group at the 3’ end of the primer.

• DNA replication requires assembly of many proteins (at least 30) at a growing replication fork: helicases to unwind, primases to prime, ligases to ligate (join), topisomerases to remove supercoils, RNA polymerase, etc.

DNA Replication Fork

DNA is unwinding

DNA Synthesis

RNA• RNA, or ribonucleic acid, is similar to

DNA, but-- RNA is (usually) single-stranded-- the sugar is ribose rather than deoxyribose

-- uracil (U) is used instead of thymine• RNA is important for protein synthesis

and other cell activities• There are several classes of RNA

molecules, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and other small RNAs

The Genetic Code

• DNA: sequence of four different nucleotides

• Protein: sequence of twenty different amino acids

• The correspondence between the four-letter DNA alphabet and the twenty-letter protein alphabet is specified by the genetic code, which relates nucleotide triplets, or codons, to amino acids

Standard Genetic Code

Variation of genetic codesT1 T2 T3 T4 T5 T6 T9 T10 T12 T13 T14 T15

CUUCUCCUACUG

LeuLeuLeuLeu

----

ThrThrThrThr

----

----

----

----

----

---Ser

----

----

----

AUUAUCAUAAUG

IleIleIleMet

--Met-

--Met-

----

--Met-

----

----

----

----

--Met-

----

----

UAUUACUAAUAG

TyrTyrStopStop

----

----

----

----

--GlnGln

----

----

----

----

--Tyr-

---Gln

AAUAACAAAAAG

AsnAsnLysLys

----

----

----

----

----

--Asn-

----

----

----

--Asn-

----

UGUUCGUGAUGG

CysCysStopTrp

--Trp-

--Trp-

--Trp-

--Trp-

----

--Trp-

--Cys-

----

--Trp-

--Trp-

----

AGUAGCAGAAGG

SerSerArgArg

--StopStop

----

----

--SerSer

----

--SerSer

----

----

--GlyGly

--SerSer

----

T1: standardT2: vert mtT3: yeast mtT4: other mtT5: invert. mtT6: cil. etc nuc.T9: ech. mtT10: eup. nuc.T12:alt yeast nucT13: asc. mtT14: flat. mtT15: bleph. nuc.

Protein Synthesis

Transcription

• Transcription is a complex process involving several steps and many proteins (enzymes)

• RNA polymerase synthesizes a single strand of RNA against the DNA template strand (anti-sense strand), adding nucleotides to the 3’ end of the RNA chain

• Initiation is regulated by transcription factors, including promoters, usually an initiator element and TATA box, usually lying just upstream (at the 5’ end) of the coding region

• 3’ end cleaved at AAUAAA, poly-A tail added

Exons and Introns• Most of the genome consists of non-coding

regions• Some non-coding regions (centromeres and

telomeres) may have specific chomosomal functions

• Other non-coding regions have regulatory purposes

• Non-coding, non-functional DNA often called junk DNA, but may have some effect on biological functions

• The terms exon and intron refer to coding and non-coding DNA, respectively

Intron Splicing

Translation

• The AUG start codon is recognized by methionyl-tRNAi

Met

• Once the start codon has been identified, the ribosome incorporates amino acids into a polypeptide chain

• RNA is decoded by tRNA (transfer RNA) molecules, which each transport specific amino acids to the growing chain

• Translation ends when a stop codon (UAA, UAG, UGA) is reached

Translation Illustrated

From Primary Transcript to Protein

Alternative Splicing (of Exons)

• How is it possible that there are millions of human antibodies when there are only about 30,000 genes?

• Alternative splicing refers to the different ways the exons of a gene may be combined, producing different forms of proteins within the same gene-coding region

• Alternative pre-mRNA splicing is an important mechanism for regulating gene expression in higher eukaryotes

Acknowledgements

• http://www.accessexcellence.org/AB/GG

•http://www.oup.co.uk/best.textbooks/biochemistry/genesvii

• Sandrine Dudoit, UC Berkeley Biostatistics

• Yee Hwa Yang, UC Berkeley Statistics

• Terry Speed, UC Berkeley Statistics and WEHI, Melbourne, Australia