Structure and Study of Macromolecules

DNA

mRNA (4%)

Proteins

transcription

translation

functional RNAs (96%)

DNA

All prokaryotic and eukaryotic genomes consist of DNA.

(Some viruses have RNA genomes, e.g influenza viruses.)

DNA (deoxyribonucleic acid)

DNA is a polymer built of deoxyribonucleotides:

Polymerization of deoxyribonucleotides into DNAis catalyzed by DNA polymerase:

Speed of synthesis in replication ≈ 2000 nucleotides/sec.

DNA in cells can be (relatively) short or long, single- or double-stranded, linear or circular.

Examples of genome organization:

Species Genome Size Number of genes

Parvovirus Single-stranded linear DNA 1.6 kb 5

Phage M13 Single-stranded circular DNA 6.4 kb 10

E. coli Double-stranded circular DNA

4,600 kb 4405

H. sapienschromosome 21

Double-stranded linear DNA 47,000 kb 584

3D-structure of DNA

Right- and left-handed DNA helices

3D-structure of DNA

Hydrogen bonds stabilize DNA double helix

Hydrogen bonds

Weak bonds between a positivelycharged donor hydrogen atom anda negatively charged acceptor atom

Hydrogen bonds in DNA

van der Waals forces

Weak attractive forces induced in atoms that are close to each other.

DNA strands can be separated (denatured) bybreaking the hydrogen bonds

Heat and OH- ions (alkali) can break H-bonds

3D-structure of DNA

Hydrogen bond acceptors and donors in the major and minor grooves of DNA

3D-structure of B-DNA

B-DNA is the predominant form of DNA in cells but not the only form

DNA is associated with proteins to form chromatin

Closed circular DNA is normally wound around itself(supercoiled).

The degree of DNA supercoiling can be determined byspecific techniques and visualized by agarose gel electrophoresis.

relaxed ccDNA

linearized ccDNA

moderately supercoiled ccDNA

highly supercoiled ccDNA

RNA

DNA

mRNA rRNA tRNA snRNA snoRNA microRNA siRNA

ribozymes

Protein synthesis

Splicingof mRNA

Processing of rRNA

Regulation of gene expression

Catalysts

RNA

DNA

tRNA

Contains uracil (instead of thymine in DNA)

Sugar-phosphate backbone containsribose (instead of deoxyribose in DNA)

Differences between DNA and RNA

2’ hydroxyl group

Uracil instead of thymine

RNA is synthezised by RNA polymerases

RNA can fold back on itself to form double helices

RNA secondary and tertiary structures

Pseudoknot

Tetraloop

tRNA secondary and tertiary structures

secondary tertiary

RNA secondary structures can be predicted

Quickfold

5’- cgggauguagcgccagcuugguagcgcaugugcuuugggagcauagggucgcagguucgaauccugucaucccga -3’

RNA

DNA

mRNA rRNA tRNA snRNA snoRNA microRNA siRNA

ribozymes

Protein synthesis

Splicingof mRNA

Processing of rRNA

Regulation of gene expression

Catalysts

Examples of ribozymes

RNase P activity

RNA

tRNA

protein

Proteins

DNA

mRNA

Proteins

CatalysisEnzymes

StructureCytoskeletonHairNails

ContractionActinMyosin

TransportHemoglobin

RegulationActivatorsRepressors

ProtectionAntibodiesToxins

StorageSeed proteins

Proteins are synthesized by polymerization of amino acids

General structure ofan L-amino acid Peptide bond formation

The 20 common amino acids specified by the genetic code

Structural organization of polypeptide chains

Rotations are possible around the C-N and C-C bonds of peptide bonds

Peptide bond

a-helices and ß-sheets are common secondary structures of proteins

a-helix ß-sheet

Examples for proteins consisting mostly of a-helices and ß-sheets

a-helix

ß-sheet

a-keratins: hair, wool, skin, horns, nails

ß-keratins: fibers of spiders and silkworm,claws, scales, and beaks ofreptiles and birds.

3D-folding of polypeptide chains is stabilized by:

Hydrogen bondsDisulfide bonds (covalent)Ionic (+ -) interactionsHydrophobic interactionsvan der Waal’s interactions

Note: in cells correct folding of proteins is promoted by chaperones and chaperonins.

Proteins can have sequence and structural motifs

Helix-turn-helix motif Zinc finger motif

Protein domains