Biological background: Molecular Biology

Class web site: http://statwww.epfl.ch/davison/teaching/Microarrays/

Statistics for Microarrays

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

Two types of organisms*

* Every biological ‘rule’ has exceptions!

Timeline of Genetics Highlights

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

Mendelian Genetics

Human Chromosomes

Human Chromosome Banding Patterns

Chromosomes and DNA

Cell Division -- Mitosis

Cell Division -- Meiosis

Crossing over and Recombination

Mitosis and Meiosis Compared

(BREAK)

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

Adenine (A) Guanine (G) (Purines)

Thymine (T) (DNA) (Pyrimidines)

Cytosine (C)

Uracil (U) (RNA)

Nucleotide Bases

Nucleotide codes

A Adenine W Weak (A or T)

G Guanine S Strong (G or C)

C Cytosine M Amino (A or C)

T Thymine K Keto (G or T)

U Uracil B Not A (G or C or T)

R Purine (A or G) H Not G (A or C or T)

Y Pyrimidine (C or T) D Not C (A or G or T)

N Any nucleotide V Not T (A or G or C)

Base Pairing

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• DNA 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 (replicate) 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 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