BiologyLectures – winter term 2008

1st year of Pharmacy study

Chemical composition of living matter – chemical basis of life. Atoms, molecules, organic compounds – carbohydrates, lipids, proteins, nucleic acids

3rd Lecture

Atoms-protons,neutrons,electrons

electrons electrons

Macroelements

H,O,C,N,P,S,Na,K,Cl,Fe,Mg

Microelements

I,Mn,F,Zn,Cu,Co,Se,.......

Bonds of atoms

MoleculesBond – ionic, covalent, polar and non-polar

metán

Sodík Chlór NaCl

H2O

ATP

- energy

- Structure of Nucleic acides

- signal molecule

Macromolecules

- sugars -saccharides

- lipids

- proteins

- nucleic acids

Sugars - saccharides

Monosaccharides

- pentose – ribose, deoxyribose- hexose – glucose, fructose, galactose

disascharides- saccharum, maltose, lactose

Sugars - saccharides

Polysaccharides - starch, glycogen, cellulose

Sugars - saccharides

glucose

glucogen

Proteins

Proteins

biogenic amino acids, names a codes

Proteins

Aspartic Acid Asp D Glutamic Acid Glu E Phenylanine Phe F Glycine Gly G Alanine Ala A Cystine Cys C Histidine His H Isoleucine Ile I Lysine Lys K Leucine Leu L Methionine Met M Asparagine Asn N Proline Pro P Glutamine Gln Q Arginine Arg R Serine Ser S Threonine Thr T Valine Val VTryptophan Trp W Tyrosine Tyr Y

Amino acids

Amino acids sequence

3-D structure

Function of protein

Geneticcode

Peptide bond

Proteins

Proteins

Folding of proteins

Amino Acid Sequence

3-D Structure

Protein Function

α, β−Helix pleadted sheet

3-D structure of proteins1. Primary structure – amino acids sequence

(determine by mRNA)

2. secondary – α-or β-helix; pleated sheet(H-bonds)

3. Tertiary – 3-D protein structure(S-S bonds)

4. Quaternary – the final structure of proteins(subunits, prostetic units and etc.)

3-D Structure of

proteins

Three ways of proteins bonds

Proteins are hungry

Amino Acid Sequence

3-D Structure

Protein Function

Nucleic acids

DNA-RNA

Nucleic acids

DNA

ChromosomeNucleus consists one or more molecules DNA organized intochromosomes

Human: – 22 pars autozomes– 1 par sex chromosome

Human karyotypes

Human and mouse chromosomes:

DNA chemical structure

Double helix of DNA

Double helix• Two complementary DNA strains

• Spring will be 52th anniversary of its discovery

Detection of DNA

Detection of DNA

Red – increase of sample transcripts

Green – increase of sample transcripts

Yellow – equal abundance

Limit of Detection: 1 in 30,000 transcripts

~ 20 transcripts/cell

Affymetrix GeneChip®

Limits: 1: 100,000 transcripts

~ 5 transcripts/cell

Affymetrix GeneChip®

Nuclear membraneChromatin fiber

} Other Chromatinfactors

H1

H1

Nuclear matrix

Nuclear pore

Nucleosomes

DNA

Chromatin fiber(30 nm dia.)

3-D Structure of DNA in nucleus

DNA-protein complex

DNAfolding

Chromatin structure

DNA is wrapped around histone proteins as chromatinChromatin structure

The Obstacles are Regulated: Histone Modifications

A Histone Code?

ChromoDomain

BromoDomain

• regulation of transcription • complex of genes to the DNA locus• protection of specific genes

All cells – the same DNA- different reading of DNA- differentiation of cells

Histones play Key role in Regulation ofgene expression

Transcription and Processing

PolyA+RNA in red(a spliceosomal component) in green Overlap (red + green) = yellow

DNA in bluePolyA+RNA in red

RNA• Ribonucleic

• Similar as DNA

• Tymine (T) is substituted by uracile (U)

• RNA can be:– One-strain helix– Double – strains helix– Hybridisated with DNA

RNA• RNA is usually one strain

• It forms the 3-D secondary and tertiary structure

• The most important is extreme variability of the RNA molecules -sequence

tRNA: sequence, 3-D structure

mRNA• Messenger RNA

• Linear molecule coded genetic information – copy from DNA

• Transcription: process of copy mRNA from DNA

mRNA modification• Eukaryotic genes are built:

• Exons: coding regions• Introns: non-coding regions

• splicing: cut of introns from molecule of mRNA and link the exons

• After this modification of mRNA is translated to sequence of protein

mRNA modification

Image source: http://departments.oxy.edu/biology/Stillman/bi221/111300/processing_of_hnrnas.htm

tRNA• Transfer RNA

• Precise 3-D structure

• The translation process of protein

tRNA structure

tRNA• Specific tRNA for each amino acid

• Determine by 3 nucleotide - anticodone(complementary with mRNA)

• Translation: process of prescription of codons of mRNA to sequence of amino acids to protein

tRNA

tRNA: sequence, 3-D structure

tRNA structure

rRNAsecondarystructure

16S ribosomal RNA

T. thermophilus - Ramakrishnan et al., Cell, 2002

Lipids

Schematic Diagram of a phospholipid molecule

(phosphatidylcholine)

Phospholipids

• Membranes of mammalian cells contain 3 major phospholipids– Classified according to the polar

headgroup

Saturated fatty acid

Unsaturated fatty acid

Differences in the length and degree of saturation of fatty acids affect their

ability to pack& hence the fluidity

of the bilayer

Choline head-group

Polar

Nonpolar

Phosphatidylcholine

Amphipathic

A, formula

B, schematic drawing

C, space-filling model

Cholesterol is oriented in the membrane between phospholipidmolecules with its polar end towards the outside surface of the monolayer and its hydrophobic end projecting into the interior of the membrane

Lodish et al, Fig 5-30