Download Water Covalent Bonds Ionic Bonds Non

BME205 Lecture
Simeon Wong | 2013 Jan 11 | 1
Water
Often macromolecules are classified by how they interact with water. Very fundamental to biological processes.
Hydrophilic: water liking
mnemonic: pedophilia (weeeeeird)
Hydrophobic: water fearing
Amphipathic: compounds that have regions that are hydrophobic and hydrophilic
Covalent Bonds
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Not generally the bonds that biologists are worried about.
When two atoms share one or more electrons.
Covalent bonds mediate interactions between atoms that make up a molecule (strong, static)
Governed by stability of atoms when outermost electron shell is filled
Electron sharing
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Bonds between atoms of the same element will share electrons equally
Non-same atoms: one of the atoms will pull electrons closer than the other.
Electronegativity: Nitrogen, Oxygen and Sulfur are strongly electronegative.
o Pull electrons closer than other atoms
Polar molecules due to electronegative atoms pulling electrons over to their side. But consider geometry as well!
Water is polar! Has an electric charge with a dipole moment. Polarity of molecules is what makes things hydrophobic/philic.
Ionic Bonds
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Attractive force between a positively charged ion and negatively charged ion.
Essentially one atom is so electronegative, they steal the electron from the
other atom.
Dissolution:
Hydration Shell
Water molecules attached to ions in hydration shell due to ionic attraction and water’s
polarity. There is an energy involved in taking the water molecules away in order to
work with the ions (with bodily processes)
Non-covalent Bonds
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Direct interactions between molecules or different parts of biomolecules and
are relatively dynamic.
Hydrogen Bonds
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For most intent and purposes, it’s like a dipole-dipole interaction
Attractive force between partially positive hydrogen with a molecular dipole
with unpaired electrons from another atom.
Represented by dotted lines
BME205 Lecture
Simeon Wong | 2013 Jan 11 | 2
Van der Waals Interactions
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Weak, non-specific attractive forces
Happens too all molecules when they come really close
All atoms have fluctuating electron distributions that oscillates and shifts and
usually there’s transient dipoles due to the electrons moving around
These transient dipoles interact and causes Van der Waals interactions
Hydrophobic Effect
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Hydrophobic molecules tend to cluster together
Important for protein folding!
Related to entropy and energetic favourability
Hydrocarbons
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Molecules composed to carbon and hydrogen. Nothing else. Tend to be hydrophobic.
o Share electrons relatively equally and thus non-polar
Won’t be asked about specifics of orgochem. (alkenes, alkynes, aromatic hydrocarbons etc)
Units
kcal: 1000 calories -> empirical unit to measure energy
mol: 6.022E23 molecules
Avogadro’s number
“M”: concentration -> 1 mole per litre
Protein-Protein interactions
Affinity: the tendency of two molecules to bind. (kd is used to quantify how well. Concentration at which interactions occur)
Specificity: describes the selectivity of the binding.
“Does protein A interact with B, and if yes, does it also interact with C? And how much C is required before it starts
interfering?”
Example
Geckos stick to smooth surfaces via van der Waal forces
Better than covalent because movement is dynamic, so the bonds are easily made and destroyed
Lots of surface area on their feet so that it sticks better.
Van der Waal forces like worker bees. Gotta have a lot of them to be powerful.
Fundamental Types of Organic Molecules
1. Proteins
2. Nucleic Acids
3. Sugars
4. Lipids
Monomers are nearly identical subunits that are covalently linked together to form polymers.
Secondary structure of macromolecules (and function) are determined by non-covalent bonds.
BME205 Lecture
Proteins
Comprised of a combination of 20 different amino acids.
Carboxyl group, and amino group. Functionality determined by differing R chain.
Bunch of amino acids together: peptide chain.
Any amino acids denoted with positive or negative charges are likely hydrophilic.
Cysteine: can form super-strong disulphide bonds.
Glycine: small amino acid, and thus allows for protein flexibility. Protein hinge.
Proline: has a ring, so it makes protein rigid around it.
Nucleic Acid
DNA and RNA
DNA is missing an oxygen in the ribose sugar component
Bases
Purines: Adenine, Guanine
Pyrimidine: Uracil, Thymine, Cytosine
Sugars
Polysaccarides
• Structure, energy storage
Lipids
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Rules in structure (lipid bilayers) and energy storage (fatty acids)
Simeon Wong | 2013 Jan 11 | 3