ZOO405 by Rania Baleela is licensed under a Creative Commons Attribution- NonCommercial-ShareAlike 3.0 Unported LicenseRania BaleelaCreative Commons Attribution- NonCommercial-ShareAlike 3.0 Unported License

Course Requirements Attendance: 15% انذار = 25% absence= حرمان من الامتحان Arrive on time: doors will be closed after 5 minutes from start

This week lectures content Macromolecules Types of bonds between macromolecules DNA: 1.Structure 2.Function 3.Properties=> compaction levels

What are macromolecules?

Complex macromolecules Covalent or noncovalent associations of more than one major classes of large biomolecules which greatly increases the functionality or structural capabilities of the complex. Nulceoprotein: nucleic acids +protein Glycoprotein: carbohydrate + protein Lipoprotein: Lipid + protein

Large macromolecular assemblies e.g. Nucleoprotein

Nucleoprotein = protein structurally associated with nucleic acid e.g. Chromatin : Histones + DNA Telomerase : (RNA + protein), Ribosome : ribosomal proteins + rRNA, Viruses : protein capsid + RNA or DNA,

4 major forces between proteins & nucleic acids 1.Electrostatic forces: salt bridges 2.Dipolar forces: hydrogen bonds 3.Entropic forces: the hydrophobic effect 4.Dispersion forces: base stacking Noncovalent bond

1. Electrostatic forces: salt bridges Long range, Not very structure-specific, Contribute substantially to the overall free energy of association. In protein- nucleic acids (NA) complexes, they occur between the ionized phosphates of the NA and either the e-ammonium group of lysine, the guanidinium group of arginine, or the protonated imidazole of histidine.

2. Dipolar forces: hydrogen bonds Dipolar, Short-range interactions Contribute little to the stability of the complex but much to its specificity. Occur between the AA side chains, the backbone amides and carbonyls of the protein, and the bases and backbone sugar-phosphate oxygens of the NA. Are very important in making sequence- specific protein-NA interactions

Favored amino acid-base hydrogen bonds Arg and Lys --- G, Asp and Glu --- A, Ser and His --- G 80% of Ser and Thr’s interactions are with the DNA backbone

3. Entropic forces: the hydrophobic effect Short range, Sensitive to structure, Proportional to the size of the macromolecular interface, Contribute to the free energy of association When molecules aggregate, the ordered water molecules at the interface are released & become part of the disordered bulk water, thus stabilizing the aggregate by releasing the entropy of the system.

Water molecules left at the interface between a protein & a NA decrease the entropy of the system. => the surface of the protein & NA tend to be exactly complementary = no unnecessary H2O molecules remain when the complex forms.

4. Dispersion forces (Van der Waals): base stacking Have the shortest range Are very important in base stacking in double- stranded NA and in the electrical interaction of protein with ssNA. Base stacking is caused by 2 kinds of interaction: 1. hydrophobic effect 2. dispersion forces.

Molecular biology the study of biology at the molecular level

Definition = the branch of biology that deals with the molecular basis of biological activity. Overlaps with genetics and biochemistry Its main concern is to understand the interactions between the various systems of a cell, including the interactions between the different types of DNA, RNA and protein biosynthesis and their regulation.

Key components Nucleotide DNA RNA Chromosome Variation Genome Heredity Mutation

Nucleotides = the building blocks of nucleic acids

Structure of DNA James Watson & Francis Crick (1953)  Double Helix  Held together by hydrogen bond  Purine with Pyrmidine Guanine – Cytosine Adenine – Thymine

DNA Is a polynucleotide that contain the sugar 2-deoxy- D- ribose Is compacted into chromosomes with the help of proteins

Ribonucleic acid (RNA) A family of large biological molecules that performs multiple vital roles in coding, decoding, regulation, and expression of genes

RNAs involved in protein synthesis

DeoxyriboNucleic Acid (DNA)

Function To carry information needed for the synthesis of proteins.

DNA is a polynucleotide that contain the sugar 2-deoxy-D- ribose Deoxyribonucleotide structure: PHOSPHATE – SUGAR – BASE Structure deoxyribose Adenine (A) Guanine (G) Cytosine (C) Thymine (T)

2-Deoxy-D-ribose sugar Why is it called 2-Deoxy?

Nucleoside structure BASE SUGAR NUCLEOSIDE

e.g. Deoxycytidine

Deoxyribonucleotide structure

Attachment of bases to sugar The glycosilic link is between carbon atom 1 of the sugar & nitrogen position 1 and 9 of the bases (purine: A & G and pyrimidine: T & C).

DNA Is slightly–ve charged, The bases are almost H2O insoluble, The phosphoric acid –OH groups are highly hydrophilic, The sugar is strongly hydrophilic,

Chromosome Structure 1.Chromatid, 2.Centromere, 3.Short arm, 4.Long arm, 5.Telomere.

Satellite DNA found at centromeres promotes correct spindle–chromosome attachments (Bassett, E.A., et al J. Cell Biol)

Telomere 1.Chromatid, 2.Centromere, 3.Short arm, 4.Long arm, 5.Telomere. 100s repeats of a simple (TTAGGG) n

Telomeres are important Consist of up to 3,300 repeats of the DNA sequence TTAGGG. Protect chromosome ends from being mistaken for broken pieces of DNA that would otherwise be fixed by cellular repair machinery. Every time cells divide the telomeres shrink. When they get short enough, cells stops dividing and our body stops making those cells. Over time, this leads to aging and death. Cells may escape death by becoming cancerous and activating an enzyme called telomerase, which prevents the telomeres from getting even shorter.

DNA compaction

Eukaryotic chromosomes Long linear DNA molecules that carry genes interrupted by intergenic regions.

DNA is complexed with proteins & organized as chromatin in the interphase nucleus:

A problem of space Human genome (in diploid cells) = 6 x 10 9 bp 6 x 10 9 bp X 0.34 nm/bp = 2.04 x 10 9 nm = 2 m/cell Very thin (2.04 nm), extremely fragile Diameter of nucleus = 5-10  m  DNA must be packaged to protect it, but must still be accessible to allow gene expression and cellular responsiveness.

The solution?

Cellular structures that contain the genetic material. Located in the nucleus. made of chromatin (=DNA +proteins) centromere telomere arm (chromatid) Chromosomes

Are the result of progressive levels of packing.  DNA in Humans= 2m  Packed in 46 chromosomes  In a 0.006mm nucleus

DNA compaction Involves interactions between DNA & various proteins: DNA= genetic material Proteins (histones & nonhistones): provide organized structure

Proteins: Histones Main packaging proteins in eukaryotes. 5 classes: H1, H2A, H2B, H3, H4. Rich in Lysine and Arginine. Positively charged=> recognition process, Binds by electrostatic interactions to the phosphate backbone.

HISTONES Very highly conserved in eukaryotes in both Structure & Function

Interaction of DNA (orange) with histones (blue). These proteins' basic amino acids bind to the acidic phosphate groups on DNA.

Histone octamer components (20% SDS-PAGE gel)

Acid extraction removes histones from meta-phase chromosomes, leaving nonhistones... Low power high power Scaffold protein DNA loops Major non-histone proteins = topoisomerases!