CS790 – Introduction to Bioinformatics

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CS790


Bioinformatics

A Gentle Introduction to

(or review of)

Fundamentals of Chemistry

and Organic Chemistry

Square one…

CS 790


Bioinformatics

CS790


Bioinformatics

Intro to biochemistry

2

Fundamentals 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

C

Carbon

12.01

Isotopes of Chlorine




Atomic

Natural


Isotope

Protons

Neutrons

mass

abundance

35
Cl

17

18

34.97

76%

37
Cl

17

20

36.97

24%

CS790


Bioinformatics

Intro to biochemistry

3

Electron shells and orbitals


Quantum numbers


n

= First quantum number = shell


l

= Second quantum number = orbital type


Golden rule:
l < n

Know these

two.

Types of Orbitals


Second

Letter

Number

Maximum


quantum

denoting

of

number of


number

orbitals

orbitals

electrons


0

s

1

2


1

p

3

6


2

d

5

10


3

f

7

14

CS790


Bioinformatics

Intro to biochemistry

4

Subshells 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

2p
5

Electron Subshells

1
st

Quantum

2
nd

Quantum

Notation for

number

number

subshells

1

0

1
s

2

0,1

2
s
,2
p

3

0,1,2

3
s
,3
p
,3
d

4

0,1,2,3

4
s
,4
p
,4
d
,4
f




CS790


Bioinformatics

Intro to biochemistry

5

Electronic configurations


Since the subshells
are filled from
lowest
to highest energy
,
we can specify only
the outermost shell.


Atoms tend to lose or
gain electrons such
that the outermost
subshell is full:
valence

CS790


Bioinformatics

Intro to biochemistry

6

Covalent 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

CS790


Bioinformatics

Intro to biochemistry

7

Covalent bonds: Lewis diagrams


How many covalent bonds will an atom form?


Flourine
:

Atomic number = 9,


Electron configuration: 1
s
2
,2
s
2
,2
p
5





Oxygen
:

Atomic number = 8


Electron configuration: 1
s
2
,2
s
2
,2
p
4

F

F

F

or

F

F

O

O

O

or

O

O

CS790


Bioinformatics

Intro to biochemistry

8

How many covalent bonds?


Note the common
valences for the
elements most
common in
proteins and
DNA:


Carbon


Oxygen


Nitrogen


Hydrogen


Sulfur


Note the similarity
between S and O.

CS790


Bioinformatics

Intro to biochemistry

9

Ions 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: 1
s
2
,2
s
2
,2
p
6
,3
s
1


Na
+


Chlorine (Cl): A# = 17: 1
s
2
,2
s
2
,2
p
6
,3
s
2
,3
p
5


Cl



Complete electron transfer, no sharing


Coulombs law:


Ionic bond

or
salt bridge

CS790


Bioinformatics

Intro to biochemistry

10

Polar 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



CS790


Bioinformatics

Intro to biochemistry

11

The 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

O

H

+

H

+




O

N

CS790


Bioinformatics

Intro to biochemistry

12

Van der Waals bonds


Nonspecific


when any two atoms at
~3 to 4 Å
apart


Å = angstrom units = 10

10

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 der

Waals contacts can become significant


CS790


Bioinformatics

Intro to biochemistry

13

Energy 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

CS790


Bioinformatics

Intro to biochemistry

14

Looking at chemical structures

CH
3

H

H

H

H

H

C

C

H

H

H

C

CH
2

CH
3

C

C

C

Propane:

C

C

C

C

C

C

H

H

H

H

H

H

Benzene:

CS790


Bioinformatics

Intro to biochemistry

15

A 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 C
4
H
10


Butane:


Isobutane:

CH
3

CH
2

CH
2

CH
3

CH
3

CH

CH
3

CH
3

CS790


Bioinformatics

Intro to biochemistry

16

Double 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

CS790


Bioinformatics

Intro to biochemistry

17

Some Common Functional Groups

CS790


Bioinformatics

Intro to biochemistry

18

Concentration


1 mole of a substance = 6.02
×

10
23

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 Na
2
SO
4
) and add enough water to make
1 liter of solution: M = [Na
2
SO
4
] = 1.0

CS790


Bioinformatics

Intro to biochemistry

19

Acids 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 H
3
O
+


Strong acids

dissociate completely


Weak acids

do not dissociate completely


pH of a solution


pH =

log[
H
+
]

CS790


Bioinformatics

Intro to biochemistry

20

More on pH


A simple example:


Suppose we add 0.001 moles of HCl to 1.0 L of H
2
0


[
H
+
] = 10

3

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

CS790


Bioinformatics

Intro to biochemistry

21

pKa


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

CS790


Bioinformatics

Intro to biochemistry

22

Properties of Water


The polarity of water makes it highly cohesive:


Water solvates & weakens

ionic and hydrogen bonds:

CS790


Bioinformatics

Intro to biochemistry

23

Hydrophobic Attraction


Nonpolar (hydrophobic atoms), are driven
together


Hydrophobic interactions


Driven by water’s affinity for itself