Lecture 1: water scale Flashcards
•A relatively simple form of life
•Unicellular
•Short life cycle, highly adaptable to environment
What am I?
Prokaryotes
•Large cells (10 to 100 um)
•Specialized membrane-enclosed organelles
•Complex structure and function at all levels
•Often multicellular
•Long life cycle, specialize in stable environments
What am I?
Eukaryotes
What are the important characteristics of carbon for life?
•Can form 4 highly stable covalent bonds
•High functionality (single, double, triple bonds with C, O, N, S, H)
•Can form C-C chains
•Oxide is a soluble gas that is chemically available
Describe Hydrogen bonding in water
•Hydrogen bonds are electrostatic interactions and are neither ionic nor covalent bonds
•Relatively weak
Why are H-bonds important in biological systems?
H-bonds….
•Allow water to dissolve polar uncharged molecules
•Can mediate interactions between molecules
What does the high dielectric constant of water allow it to do?
•Dissolve ions and polar compounds
Water is a reactant in biochemical processes. What does this mean?
•It has acid/base properties
•it is often a direct participant in biochemical reactions
What are the types of Non-covalent bonding?
• Ionic bonding
• Hydrogen bonding
•Hydrophobic interactions
•Van der Waals interactions
Characteristics of Prokaryotic cells
Are single cell organisms that can be separated into Bacteria and Archea groups. They can be Gram Negative or Gram Positive. Have no membrane enveloped nucleus and has a very fast evolution time scale. They are very adaptable to environmental changes and situational challenges.
Characteristics of Eukaryotic Cells
They are large cells compared to bacteria, have multiple membrane-enclosed organelles including the nucleus, which contains genetic information. Organelles have distinct functions (Mitochondria, Golgi, ER) They have a longer evolutionary time scale and provide biologically relevant models in disease and cancer research
Carbon bond characteristics
•Tetrahedral arrangement of four single bonds
•Free rotation about the carbon-carbon bond (if single bond)
•Double and Triple bonded carbon-carbon bonds are shorter and do not have free rotation
Characteristics of Water
Able to hydrogen bond with other water molecules and can give rise to internal cohesion in liquid form. It has a relatively high boiling point for a small molecule and the hydrogen atoms are oriented at a near tetrahedron orientation around the oxygen atom. The difference in electronegativity creates a dipole that is partially negative and partially positive
Liquid Form
Water is mostly disorganized and in continuous motion. Even though each molecule in solution can for 4 hydrogen bond (on average only 3.4 hydrogen bonds are formed)
In solid form
Static molecules, all hydrogen bonds formed
Hydrogen bonding in biomolecules
Stability of biomolecules, enzyme-substrate recognition and binding and DNA and RNA double strand
Water as Solvent
Water surrounds the Na+ and Cl- ions, weakening the electrostatic interaction between them. The high dielectric constant of water allow it to readily dissolve polar compounds
Amphiphatic molecules
Composed of a polar and non polar group (phospholipids). Hydrophobic effect drives the nonpolar region together. Polar groups can interact with water and clustering of the nongroups forms a micelle (hydrophobic effect) it’s the driving force of biomolecular membranes
Water in Enzymatic reactions
Participates in Enzymatic reactions
Water in protein-DNA interactions
The DNA binding protein, trp repressor, uses water molecules bound to the DNA as a recognition motif, recognizing specific DNA sequences. Mutations to the DNA and/or protein that alter binding of the water (DNA mutants) or recognition of the water by the protein (protein mutant) attenuates DNA binding
Hydrogen bonding
Occurs between H-bond and acceptor
Ionic/electrostatic interactions
Occurs between oppositely charged atoms
Hydrophobic/hydrophobic effect
Packing of hydrophobic molecules together
Van der waals
Distance-dependent interaction of dipoles in atoms
