cs790 – bioinformatics a gentle introduction to (or review of) fundamentals of chemistry and...
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CS790 – Bioinformatics
A Gentle Introduction toA Gentle Introduction to(or review of)(or review of)
Fundamentals of ChemistryFundamentals of Chemistryand Organic Chemistryand Organic Chemistry
Square one…
CS 790 – BioinformaticsCS 790 – Bioinformatics
Intro to biochemistry 2CS790 – Bioinformatics
Fundamentals of ChemistryFundamentals of Chemistry Reading the periodic table Neutrons and isotopes
Electron shells, subshells and orbitals• Each orbital can hold at most 2 electrons• In the ground state orbitals are filled from lower to
higher energy
6
CCarbon
12.01
Isotopes of ChlorineAtomic Natural
Isotope Protons Neutrons mass abundance35Cl 17 18 34.97 76%37Cl 17 20 36.97 24%
Intro to biochemistry 3CS790 – Bioinformatics
Electron shells and orbitalsElectron shells and orbitals Quantum numbers
• n = First quantum number = shell• l = Second quantum number = orbital type• Golden rule: l < n
Know theseKnow thesetwo.two.
Types of OrbitalsSecond Letter Number Maximum
quantum denoting of number ofnumber orbitals orbitals electrons
0 s 1 21 p 3 62 d 5 103 f 7 14
Intro to biochemistry 4CS790 – Bioinformatics
Subshells and valenceSubshells and valence All orbitals of the same type (same l and n) are
called a subshell Subshell
notation:Electron
shell
# electrons in the subshell
Type of orbitals
2p5
Electron Subshells1st Quantum 2nd Quantum Notation fornumber number subshells1 0 1s2 0,1 2s,2p3 0,1,2 3s,3p,3d4 0,1,2,3 4s,4p,4d,4f
…
Intro to biochemistry 5CS790 – Bioinformatics
Electronic configurationsElectronic configurations Since the subshells
are filled from lowest to highest energy, we can specify only the outermost shell.
Atoms tend to lose or Atoms tend to lose or gain electrons such gain electrons such that the outermost that the outermost subshell is full: subshell is full: valencevalence
Intro to biochemistry 6CS790 – Bioinformatics
Covalent BondsCovalent Bonds For almost all of the
elements that we will deal with, 8 valence electrons is an electronically stable configuration.
Covalent bonds are formed when atoms share electrons to fill the valence shell
Intro to biochemistry 7CS790 – Bioinformatics
Covalent bonds: Lewis diagramsCovalent bonds: Lewis diagrams How many covalent bonds will an atom form? Flourine: Atomic number = 9,
Electron configuration: 1s2,2s2,2p5
Oxygen: Atomic number = 8Electron configuration: 1s2,2s2,2p4
F F F or F F
O O O or O O
Intro to biochemistry 8CS790 – Bioinformatics
How many covalent bonds?How many covalent bonds? Note the common
valences for the elements most common in proteins and DNA:• CarbonCarbon• OxygenOxygen• NitrogenNitrogen• HydrogenHydrogen• SulfurSulfur
Note the similarity Note the similarity between S and O.between S and O.
Intro to biochemistry 9CS790 – Bioinformatics
Ions and ionic bondsIons and ionic bonds Formation of ions
• Conflicting goals: neutral charge vs. stable electronic configuration
• Some atoms have a strong tendency to gain or lose electrons:
Sodium (Na): Atomic # = 11: 1s2,2s2,2p6,3s1 Na+
Chlorine (Cl): A# = 17: 1s2,2s2,2p6,3s2 ,3p5 Cl–
• Complete electron transfer, no sharing
Coulombs law: Ionic bond or salt bridge
2force
d
Intro to biochemistry 10CS790 – Bioinformatics
Polar BondsPolar Bonds In reality, some atoms will attract
shared electrons more strongly. That is, the shared electrons will be “off center”.
The tendency to attract electrons is called electronegativity.
There is a continuum between covalent bonds and ionic bonds.
K I K+ I –
Intro to biochemistry 11CS790 – Bioinformatics
The Hydrogen BondThe Hydrogen Bond When hydrogen forms a polar bond, the
nucleus is left without any unshared electrons• It can make a secondary bond with another negative
ion, called a hydrogen bond• Very common in water:• Weaker than polar and
covalent bonds• Donor: covalent/polar bond to H• Acceptor: ionic attraction to H
OH+
H+
–
O N
Intro to biochemistry 12CS790 – Bioinformatics
Van der Waals bondsVan der Waals bonds Nonspecific – when any two atoms at ~3 to 4 Å
apart• Å = angstrom units = 1010 meters = 0.1 nm
Low energy interaction• Significantly smaller than
h-bonds or ionic attraction• Adds up over many atoms• When two atoms have very
similar shapes, the Van derWaals contacts can become significant
Intro to biochemistry 13CS790 – Bioinformatics
Energy of molecular interactionsEnergy of molecular interactions 1 calorie = the amount of energy to raise the
temperature of 1g of water from 14.5 to 15.5°C Molecules have about 0.6 kcal/mole of energy
from heat/vibration Molecular interactions:
• C–C : 83 kcal/mole• Electrostatic and hydrogen bonds: ~3 – 7 kcal/mole• Van der Walls interaction: ~1 kcal/mole
Intro to biochemistry 14CS790 – Bioinformatics
Looking at chemical structuresLooking at chemical structures
CH3
H
H
H H
HC C
H H H
C
CH2 CH3
C C C
Propane:Propane:
C
C C
C
C C
H H
H H
H H
Benzene:Benzene:
Intro to biochemistry 15CS790 – Bioinformatics
A hydrocarbon isomerA hydrocarbon isomer Carbon can make 4 covalent bonds
• There are more carbon-based compounds present on earth than the total of all compounds lacking carbon
• We could spend an entire course examining the properties of hydrocarbons: molecules made up only of carbon and hydrogen.
Example: Isomers of C4H10
• Butane:
• Isobutane:
CH3 CH2 CH2 CH3
CH3 CH
CH3
CH3
Intro to biochemistry 16CS790 – Bioinformatics
Double BondsDouble Bonds Double bonds can force a molecule or
functional group to be planar:
Geometric isomers• cis = on the same side• trans = on the opposite side
Intro to biochemistry 17CS790 – Bioinformatics
Some Common Functional GroupsSome Common Functional Groups
Intro to biochemistry 18CS790 – Bioinformatics
ConcentrationConcentration 1 mole of a substance = 6.02 × 1023 atoms or
molecules of that substance• C – atomic weight = 12, one mole = 12 grams
We express concentration in molarity or moles/liter.• Denoted [x].• Example – If we take 1 mole of sodium sulfate
(142.1g of Na2SO4) and add enough water to make 1 liter of solution: M = [Na2SO4] = 1.0
Intro to biochemistry 19CS790 – Bioinformatics
Acids and BasesAcids and Bases Acids give off protons in solution
• HCl H+ + Cl
• In water, the H+ ion often binds with water to form a hydronium ion H3O+
• Strong acids dissociate completely• Weak acids do not dissociate completely
pH of a solution• pH = log[H+]
Intro to biochemistry 20CS790 – Bioinformatics
More on pHMore on pH A simple example:
• Suppose we add 0.001 moles of HCl to 1.0 L of H20
• [H+] = 103 moles/liter, so pH = 3
0 7 14 acidic basic
Bases accept H+ ions• pOH = log[OH ]
pH + pOH = 14• Water: pH = 7, pOH = 7
Intro to biochemistry 21CS790 – Bioinformatics
pKapKa For a weak acid, the pKa is a measure of the
tendency of the acid to dissociate (give of an H+ ion)
Key rule:• pH = pKa : protonated and unprotonated forms are
at equilibrium• pH < pKa : more protonated• pH > pKa : less protonated
Biological pH varies but is generally close to neutral (7.0) or slightly acidic
Intro to biochemistry 22CS790 – Bioinformatics
Properties of WaterProperties of Water The polarity of water makes it highly cohesive: Water solvates & weakens
ionic and hydrogen bonds:
Intro to biochemistry 23CS790 – Bioinformatics
Hydrophobic AttractionHydrophobic Attraction Nonpolar (hydrophobic atoms), are driven
together• Hydrophobic interactions• Driven by water’s affinity for itself
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