cs790 – bioinformatics a gentle introduction to (or review of) fundamentals of chemistry and...

CS790 – Bioinformatics

A Gentle Introduction toA Gentle Introduction to(or review of)(or review of)

Fundamentals of ChemistryFundamentals of Chemistryand Organic Chemistryand Organic Chemistry

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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%


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


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

…


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


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


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


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.


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

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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 –


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


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


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


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:


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


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


Some Common Functional GroupsSome Common Functional Groups


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


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+]


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


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


Properties of WaterProperties of Water The polarity of water makes it highly cohesive: Water solvates & weakens

ionic and hydrogen bonds:


Hydrophobic AttractionHydrophobic Attraction Nonpolar (hydrophobic atoms), are driven

together• Hydrophobic interactions• Driven by water’s affinity for itself

cs790 – bioinformatics a gentle introduction to (or review of) fundamentals of chemistry and...

Documents

cs790 bioinformaticsintro

valence slide

valence electrons

bioinformatics slide

valence shell slide

f slide

electron subshells

electron configuration