Biochemistry LFS251

Week 1

Introduction & Water

Dr. Fraser Russell

E-mail: [email protected]
Telephone 4665

Office: Tower, Level 3, Rm 3.04

 Biochemistry
The Molecular Basis of Life

What can you expect from this course?

Lectures

These will be delivered by:

Dr. Fraser Russell (course coordinator)

& Dr. Felicity Lose

Contact details:

Dr. Fraser Russell

Tower, Level 3, Room 3.04
Tel: 5459 4665
E-mail: [email protected]
Lectures
13 Lectures this semester
Thursdays, LT7: 8.00 - 10.00 am

We will be learning about:

 The structure of water

 Acids and bases

 Biomolecules: Nucleic acids

Carbohydrates
Proteins
Lipids
We will be learning about:

 Metabolic pathways for energy production

Glycolysis, TCA cycle, Oxidative
phosphorylation

 Regulation of metabolism

 Fatty acid oxidation (beta-oxidation)

 Nitrogen metabolism
The Prescribed Text

Biochemistry
Garrett and Grisham, 5th Ed.

Also, obtain your practical manual

 Lab sessions: These are compulsory!

You must wear:

 Closed in shoes
 Lab coat
 Safety glasses

and bring your Prac manual & Calculator, and

completed induction form.
• Attendance at laboratory sessions is mandatory
• Notebooks must be maintained satisfactorily, and
signed by a lab demonstrator on completion of
the experiment
 Labs

6 Lab sessions this semester

Wednesdays & Thursdays even weeks,

Teaching Lab:

Wednesday pm: 6.00 pm. - 8.30 pm

Thursday am: 10.00 am - 12.30 pm

Thursday pm: 1.30 pm - 4.00 pm

First lab is in Week 2 on March 12 & 13.

Please read Prac. 1 before the class
 Tutorials

1 hr / fortnight, odd weeks

10 am -11 am DG.47/48
11 am -12 pm DG.47/48
2 pm – 3 pm DG.46
3 pm – 4 pm DG.47/48
4 pm – 5 pm DG.47/48

First Tutorial is Today (6 March)

Assessment Items Weighting

Problem Set 10%

(Biomolecules; due 4 pm Thursday, Week 5).
The problem set is now available on BB.

Practical Report 20%

Results & Discussion section
(Due 4 pm to collection box; Thursday Week 7)

Mid-semester exam 30%

(Wed 30 April & Thur 1 May, Week 8; normal lab time)

End-of-semester exam 40%

(Centrally administered exam period)
 Communication

 Learning material will be placed on Blackboard

Eg. Learning objectives

Tutorial worksheets
(print & bring to your tute class)
Lecture notes
Pod-casts

 You may contact me via e-mail, telephone or

drop by my office

 Check BB Announcements regularly.

 I may need to email you (I use BB email system)
Questions ?
 Week 1: Introduction & Water

Topics covered in this lecture

 Introduction to Biochemistry
 Electron configuration
 Ionic bonds
 Covalent bonds
 Structure of water

 Water and the hydrogen bond

 Water: an effective solvent
 Amphipathic compounds and the lipid bilayer
 Ionization of water
 What is Biochemistry ?
Biochemistry describes
the processes of life
Structure /
Function Information

Biochemistry
Figure 1.04 Structure of human endothelin.

Bioenergetics

Figure 16.04 Elements of a signal transduction pathway.

Chapter 13 Opener.
“We found that we landed right on an ancient streambed, where
water was once flowing kind of up to your kneecaps.”
Ashwin Vasavada, Deputy Project Scientist, “Curiosity” Rover expedition, 2013.

Water on Mars
Curiosity Rover, NASA
Water is essential for life
 A brief review of atoms and bonds

Electrons - Surround the nucleus

Atoms Protons
Form the nucleus
Neutrons

Mass number
Oxygen
Number of protons + neutrons

Atomic number
16
8O
Number of protons
 A brief review of atoms and bonds
Protons Neutrons Mass N Electrons
(Atomic N)

Hydrogen 1 0 1 1

Carbon 6 6 12 6

Nitrogen 7 7 14 7

Oxygen 8 8 16 8

Note: Number of electrons (-ive charge)

= Number of protons (+ive charge)
 Quantum mechanical model
Energy level (shell):
region around the nucleus
where the electron is likely 1s
to move (1, 2, 3...)
2s
Sublevels (subshell):
repulsion by electrons 2p
creates sublevels. Shell 1
has 1 subshell (1s), shell 2
has 2 subshells (2s, 2p),
shell 3 has 3 subshells
(3s, 3p, 3d) etc.
From Chemistry, Addison-Wesley. Fig 13.4
 Electrons are located in specific regions
of the subshells, called orbitals
1s
s subshells have 1 orbital
p subshells have 3 orbitals
d subshells have 5 orbitals 1s
2s
Eg.
Subshell Orbitals 2px
1s 1
2s 1 2py
2p 3
3s 1
3p 3 2pz
3d 5 From Chemistry, Addison-Wesley. Fig 13.4
 Overlap can occur (eg. 4s has lower energy than 3d)

3d
Energy level 3
4s
3p

3s 2p Energy level 2

2s
Energy level 1
1s
 Aufbau diagram shows energy levels of the
atomic orbitals
Energy
level
3p
Increasing 3
energy 3s
level
2p
2
2s
1 1s

 A maximum of 2 electrons fill each orbital

 Electrons fill orbitals of lower energy level first
 Electron configuration
A 2p atomic
3 orbital within
Energy
 3s shell 2
Levels
(shells)
   2p
2
 2s There are 11
1 electrons in this
 1s
example

Each arrow indicates an electron (e-)

 Maximum of two electrons/atomic orbital
Note: up / down represents opposite spin
 A brief review of atoms and bonds
Ionic Bonds
23
11 Na Sodium

11 Protons, therefore 11 electrons

For Sodium Energy

1s22s22p63s1 level
3  3s
The highest energy level
is 3    2p
2
 2s
1 electron in highest E.L.
(ie. 1 valence electron) 1  1s
 The Octet Rule

 In forming compounds, atoms achieve

the electron configuration of a noble gas

ie. 8 electrons in the highest energy level

 This is achieved by atoms either gaining

or losing electrons
 Sodium atom Sodium ion

Na . Na+
Loss of 1e-
Energy Energy
level level
3  3s 3 3s
   2p    2p
2 2
 2s  2s

1  1s 1  1s
11 protons & 11 electrons 11 protons & 10 electrons
 A brief review of atoms and bonds
Ionic Bonds
35
17 Cl Chlorine

17 Protons, therefore 17 electrons

Energy
For Chlorine level
1s22s22p63s23p5    3p
3
 3s
The highest energy
level is 3    2p
2
 2s
7 electrons in level 3
1  1s
 Chlorine atom Chloride ion

: Cl . -

:
: Cl :

:
Gain of 1 e-
Energy Energy
level level
   3p    3p
3 3
 3s  3s
   2p    2p
2 2
 2s  2s
1  1s 1  1s
17 protons, 17 electrons 17 protons, 18 electrons
 Sodium & Chloride ions have opposite charges

Force of attraction are ionic bonds

1s22s22p63s1 Na .
- + - +
. + - + -
1s 2s 2p 3s 3p
2 2 6 2 5 :
: Cl
: - + - +

+
1s22s22p6 Na
octet -

:
: Cl :
1s 2s 2p 3s 3p
2 2 6 2 6

:
 Ionic bonds normally form between
metal atoms (Eg. sodium) and non-
metal atoms (Eg. Chlorine)

- + - +
+ - + -
- + - +

+ Na+
http://www.beyondbooks.com/psc92/3b.asp
- Cl-
http://
www.accessexcellence.org/
RC/VL/GG/cov_IonicBs.html
 Covalent bonds
Some atoms share electrons

Shared pair of e-

H . + .H H :H
Energy Energy
level level  1s
1  1s 1  1s  1s

Sharing of a pair of electrons is 1 covalent bond

H H H2
 Covalent bonds
The sharing of
electrons allows
atoms to achieve
noble-gas electron
configuration

1 Shared pair of e-

H :H http://
 1s www.accessexcellence.org/
RC/VL/GG/cov_IonicBs.html

 1s

http://www.beyondbooks.com/psc92/3b.asp
 Covalent bonds
Nitrogen must share 3 pairs of electrons

ie. Formation of a triple covalent bond

. .
.. N . + . N .. .. N ...... N ..
. .
1s 2s 2p
    
N N O2
Sharing 3 pairs of e-     
is 3 covalent bonds
 Water
2 Hydrogen atoms share electrons with 1 oxygen atom

H.

:
+ :O:H
:O.
:

. H.

:
+ H
1s 2s 2p
Oxygen     

Hydrogen  
Hydrogen
Representations of Water

H 2O O
Unnumbered, page 26 (1) The water molecule is polar.

H H Ball-and-stick
Formula model
Bond-line
structure


O  H


H Space-filling
model
Electron-dot structures
 Week 1: Introduction & Water
Topics covered in this lecture

 Introduction to Biochemistry
 Electron configuration
 Ionic bonds
 Covalent bonds
 Structure of water

 Water and the hydrogen bond

 Water: an effective solvent
 Amphipathic compounds and the lipid
bilayer
 Ionization of water
Electronegativity: Measure of the pull of an atom
on its electrons

Oxygen has > electronegativity than Hydrogen

In water, the electrons are not shared

equally between O & H

O has a stronger pull than H. Therefore

water has an uneven distribution of charge
 Electronegativity:
O = 3.5
H H = 2.1
Li Be B C N O F
Na Mg Al Si P S Cl
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br

Beyond Books, Apex Learning Inc.

“Rules of the Atomic Playground: Polar Covalent Bonds
http://www.beyondbooks.com/psc92/3c.asp

3.0-4.0
Values calculated
Electronegativity: 2.0-2.9
by Linus Pauling
1.5-1.9 (arbitrary units)
<1.5
 Electronegativity:

 Electroneg. difference means greater bond polarity

If the electronegativity difference is >2, then it is likely

that the more electronegative atom will completely
pull the electron away from the other atom

ie. formation of an ionic bond

Na = 0.9
Difference = 2.1
Cl = 3.0
 O H

Unnumbered, page 26 (1) The water molecule is polar.

http://www.beyondbooks.com/psc92/3b.asp

H = 2.1
Difference = 1.4
O = 3.5

The more electronegative atom (Oxygen) becomes

partially negatively charged. The atom with the
lower electronegativity (Hydrogen) becomes partially
positively charged

Note: There is no net charge

 H2O Hydrogen bonds:
Makes water stick together

Symbol shows partial –ive charge

Partially positive H aligns with

partially negative atom
(oxygen).
This is a Hydrogen bond

H2O
Unnumbered, page 26 (2) A hydrogen bond.

Symbol shows partial +ive charge

H2O bonds up to 4 water molecules (mean= 3)
(number decreases with  temperature)

H bond

Figure 2.03 Structure of ice.

Ice: about 4 H bonds/water

molecule. Crystalline lattice
 Bonds / Interactions

Covalent bond

Bond Unnumbered, page 28 (1) van der Waals radii.

strength
KJ.mol-1
Unnumbered, page 26 (2) A hydrogen bond.

Ionic interaction

Hydrogen bond
Figure 2.05 Relative strengths of bonds in biological molecules. Unnumbered, page 28 (1) van der Waals radii.
? Identify the type of bonding between pairs
of atoms & molecules

Electronegativity
K+Cl- K 0.8
H 2.1
Cl 3.0
O 3.5
O
O H H
H H
? Identify the type of bonding between pairs
of atoms & molecules

Electronegativity
K+Cl- Ionic K 0.8
H 2.1
Cl 3.0
Hydrogen bond O 3.5
O
O H H
H H
Covalent bond
 Summary

Hydrogen bond: Between H

atom covalently bonded to an
electroneg. atom, and a second
electroneg. Atom eg. N, O, S

Covalent bond: Bond in which 2

atoms share a pair of electrons
Unnumbered, page 26 (2) A hydrogen bond.

Ionic bonds: Interactions

between oppositely charged +
Na -

:
atoms/groups : Cl :

:
 Water is an effective solvent: Role of H bonds

Unnumbered, page 29 (2) Hydrated solutes.

 The ion-dipole interaction between Na+ (or Cl-) &

water is stronger than ionic interactions between
Na+ and Cl-

 The ions therefore dissolve in water to form a solute

 Also dissolves glucose (stored as glycogen)

 Hydrophilic Molecules

Water Loving

Uncharged polar
molecules also
dissolve in water

Eg. glucose
Non-polar molecules usually don’t dissolve in water

Lack of ion or polar

Why? group means that the
molecule does not
interact with water
Eg. hydrocarbons

Water forms a “cage”

around the hydrocarbons

Hydrophobic Molecules

Water Fearing
Water molecules are highly ordered.
Non-polar molecules will cluster in water → Less
surface area of the cage c.f. combined surface area
of cage around individual non-polar molecules.
Some compounds have one end hydrophilic, &
the other end hydrophobic

ie. Amphipathic

Both ends Loving

 Real-World Example

Alkali metals of long chain fatty acids

Soap Eg. sodium palmitate

CH3(CH2)14COO-Na+

Hydrophobic Hydrophilic

Grease & oil (H2O insoluble) is

trapped inside the micelle, and
washed away
Amphipathic compounds may also form lipid bilayers

Extracellular
Lipid bilayers are important
to the formation of the cell
plasma membrane

 Cell structure
 Ion gradients

Intracellular
Conc. (mM) How does the cell maintain
the ion gradient?

Extracellular

Conc. (mM)
Figure 2.13 Ionic composition of intracellular and extracellular fluid.

Na+ K+ Cl-

Intracellular
Figure 2.13 Ionic composition of intracellular and extracellular fluid.

Na+ K+ Cl-
 The ion
gradient is
maintained
by ion
channels,
exchangers
& pumps

n e
a
br
em
m
a
m
l as
P
 Summary

 Ionic & polar compounds are hydrophilic (water

loving). These dissolve in H2O

 Uncharged, non-polar compounds are

hydrophobic (water fearing). These don’t
dissolve in H2O

 Amphipathic compounds form micelles or

bilayers
 Water
Introduction to Acid-Base

 Water can ionize Reversible

reaction

H2O H
+
+ OH
-

In practice, aqueous solutions don’t contain lone

protons. They contain hydronium ions (H 3O+)

+ -
H2O + H2O H3O + OH
 Water
H2O
+
H + OH
-
5.108 : 1

 Water dissociates into acid (H+) and base

(OH-). The equilibrium is to the left-hand-side

 Water has a low tendency to ionize, & the

concentration of H+ and OH- is  small

ie. very little acid or base is present

If acid and base is combined, this will form H 2O

+ - H2O
H + OH
 H2O H
+
+ OH
-

The concentration of H+ and OH- are equal in

pure water (25C)

[H+] = 10-7 M, [OH-] = 10-7 M

ie. The solution is neutral, as neither acid nor

base are in excess

 The equilibrium constant (K) for ionization of H2O

describes the tendency of water to ionize
[H+] [OH-]
K=
[H2O]
 Concentration of water:
1 litre of water weighs 1000 g
18 g of water makes 1mol (ie. MW is 18 g/mol)

Therefore in 1000 g (ie. 1 litre) of water there

is = 55.5 mol/L ie. 1000 mol L
18
Value of K (from experimental data) = 1.8 x 10 -16 mol/L
(K is the equilibrium constant for ionization of H 2O)
Kw = K x [H2O] = [H+] [OH-]

1.8 x 10-16 mol/L x 55.5 mol/L = 10-14 mol2/L2

Kw (ion product constant for water)
 [H+] [OH-] = 10-14 mol2/L2

Following ionization of water, there are equal

concentrations of [H+] [OH-]

[H+] = [OH-] =  10-14 mol2/L2

= 10-7 mol/L

This is a small number: 0.0000001 mol/L

 pH = - log [H+]
pH = - log 10-7 mol/L

= - (-7)
= 7 (this is easier to work with than 10 -7)

If [H+] increases, [OH-] decreases (& vice versa)

Eg. If [H+] = 10-6 M:

10-14 mol2/L2 = 10-8 mol/L
then [OH-] =
10-6 mol/L

(recall Kw = [H+] [OH-] = 10-14 mol2/L2)

? What is the pH when [OH-] = 10-9 mol/L
? What is the pH when [OH-] = 10-9 mol/L

Kw = [H+] [OH-] = 10-14 mol2/L2

Rearrange: [H+] = 10-14 mol2/L2

[OH-]

10-14 mol2/L2 = 10-5 mol/L

=
10-9 mol/L
pH = - log [H+]
pH = - log 10-5
pH = 5
 Further Reading:

Garrett & Grisham, Biochemistry

Chapter 2 & 9

Next Week
Acid-Base
Garrett & Grisham, Biochemistry
Chapters 2 & 4