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 1.Attendance انذار = %15 * 25% Absence حرمان من االمتحان = 2. Arrive on time: doors will be closed 5 minutes from start 3. Do participate 4. Do your assignments

This week  Macromolecules  Types of bonds between macromolecules  Molecular biology  RNA  DNA: 1. Structure 2. Function 3. Compaction levels

What are macromolecules? Very large molecules commonly created by polymerization of smaller subunits. They are typically composed of 1000s or more atoms

Human Hemoglobin α (red) and β (blue) subunits and the iron-containing heme groups in green. Source: Boundless. “Types and Functions of Proteins.” Proteins

DNA & RNA

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

Complex macromolecules e.g. Ribosomes Membranes Cellular organelles Viruses and non-biologic nanoparticles

Nulceoprotein: nucleic acids +protein 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

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

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

 Definition  Key component: Nucleotides DNA RNA Chromosome Variation Genome Heredity Mutation

DNA structure

RNA structure

Facts and a problem

The solution?

Satellite DNA found at centromeres promotes correct spindle–chromosome attachments

Not only do telomeres protect the ends of chromosomes, they also modulate gene expression over cells’ lifetimes

Home work 1 Go to ticles/PMC /pdf/nihms pdf ticles/PMC /pdf/nihms pdf Download this paper Read it We will discuss it on Thursday