Section1 Water 16

CHEM2360/MBIO2360
Biochemistry I
Biomolecules and an Introduction to

Metabolic Energy
Fall 2016 1
Introduction to Biochemistry
Instructors for CHEM 2360 and MBIO 2360

Lectures A01 Lectures A02
Dr. Brian Mark Dr. Sean McKenna
127 Buller Building 380 Parker Building
Brian.Mark@umanitoba.ca Sean.McKenna@umanitoba.ca
Office hours: By appointment Office hours: By appointment
Laboratories
Dr. Ellert Nichols
406B Parker Building
Ellert.Nichols@umanitoba.ca
Office hours: MWF 11 AM to noon, Tues & Thurs 12:30 to 1:30
2
Fall 2016
1
Textbook: Lehninger Principles of Biochemistry, 6th Edition by

Nelson and Cox
Review the material in the first chapter of the text to refresh
your memory of general chemistry and cell biology.
Lab Book: Bookstore (make sure you have 2016 Fall edition).
Lecture notes are available on UM Learn to all registered
students in CHEM/MBIO 2360. Both lecture sections will
be using these notes, but note that revisions may be made
during the course, and what is presented in class takes
precedence over the web notes.
3
Fall 2016
Information about the first lab

1. Labs begin the week of September 12th.
2. They are held in the Parker Building Rooms 406, 416, 422 and 428.
3. Lockers are NOT assigned but are available on a first come first served
basis.
4. Experiments are done in pairs so students work with whoever is in the
locker beside them. If two students are planning to work together they must
arrive together.
5. The lab schedule is in the lab manual together with information about the
lab. Students should read through this information.
6. Students require a lab coat. These can be purchased from the Chem Club in
the entry hall to the Parker Building at times that are posted.
7. Students will also eventually require a USB key to store data from
experiments.
4
Fall 2016
2
Lab Exemption Policy
To receive a future Lab Exemption, a student must:
1. Complete the Laboratory (practical + lab exam) with an overall

grade in the Laboratory portion of the course no less than 70.0 %.
2. Complete the course (i.e. a VW is not allowed if you wish to

remain eligible for a future lab exemption).
There is no deferred Lab Exam- No Exceptions!
5
Fall 2016
Evaluation:
wLaboratory- Practical 17.5%
wLaboratory- Exam (Dec 5, 6:30pm) 12.5%
wTake home Mid-Term (Oct. 25-27) 10%
wFinal Exam (TBA) 60%
Students must complete the laboratory (practical +
exam) with a grade of at least 15/30 to get credit for
the course.
6
Fall 2016
3
NEW FOR 2016.

A take-home midterm exam (10%) will be distributed in
your scheduled lecture section (A01 or A02) on Tuesday
Oct. 25th and returned to the same section Thursday Oct.
27. No exceptions
You must complete the exam alone and not consult with

other individuals regarding any aspect of the exam.
There is no deferred midterm exam. For students who
do not complete the midterm exam, the final exam will be
pro-rated to 70%.
7
Fall 2016
Four Main Groups of biomolecules:

1. Proteins (peptides or polymers of amino acids)
Enzymes, signal transduction, structural
2. Lipids
Structural, energy storage, hormones, etc.
3. Carbohydrates (monosaccharides and polysaccharides)
energy storage and cell signaling, structural
4. Nucleic Acids (DNA, RNA, nucleotides)
storage of genetic information, structural, energy storage,
energy metabolism
8
Fall 2016
4
Biochem I CHEM/MBIO 2360 covers each

of these classes of molecules, looking at their
chemical structures and molecular
functions.
Biochem II CHEM/MBIO 2370 covers their
roles in metabolism, which is the organized
network of reactions occurring in living cells.
9
Fall 2016
Organization of the 2360 Course

First Half of Course: 1) Water
2) Amino Acids
3) Protein Structure
4) Enzymes
5) Carbohydrates
Second Half: 6) Nucleic acids
7) Lipids
8) Bioenergetics
9) Glucose Metabolism 10
Fall 2016
5
Genes and proteins
The DNA genome
Genes
Transcription
mRNA
Translation
Proteins
Griswold, A. (2008) Nature Education 1(1):57
Genome sequencing projects provide scientists with the parts11

lists containing instructions for how an is organism built.
Fall 2016
What are we going to focus on?

www.scienceclarified.com/Bi-Ca/Brain.html
www.hybridmedicalanimation.com
We have about one

hundred billion neurons
in our brains!
Atomic
structure
of this
machine
Cellular citizens the

protein machines
12
Fall 2016
6
Viruses are highly structured and complex too!
www.cdc.gov
www.cgl.ucsf.edu/chimera/ImageGallery/ 13
Fall 2016
Inside the cell
14
Fall 2016
7
Biochemistry is
principally concerned
with the chemistry and
molecular interactions
of biological molecules
associated with living
systems.
15
Fall 2016
Bios = life (Greek)

al kimya = the transmutation (Arabic)
Chemistry explains change using atoms.
All chemical change involves rearrangements
of electrons.
Biochemistry explains life in terms of atomic
structures of biological molecules.
16
Fall 2016
8
Biosphere contains more than 106 different

species ranging from single cells to complex
animals. (NEW: 8.7 1.3 million eukaryotes alone! - 86% of
land species and 91% of marine species remain to be discovered!)
All life forms use the same types of
biomolecules and all share some common
metabolic features.
This suggests a common ancient ancestor.
Variations on a Theme over time
Change = Chemical Reactions 17
Fall 2016
Most biochemical reactions are mediated by enzymes.

Enzymes are proteins that catalyze biochemical
reactions.
Their catalytic activity is a function of their
molecular structure.
Proteins are composed of amino acids.
To understand the properties of amino acids (and most
other biochemical molecules) we must review water,
buffers and pH.
18
Fall 2016
9
Synthesis and degradation of biomolecules and other

transformations associated with life:
Metabolism: Organized network of reactions

occurring in cells.
1) Catabolism: Reactions that degrade nutrient
molecules yielding energy.
2) Anabolism: Cell components are assembled
from small molecules and energy.
19
Fall 2016
Bond strength depends on the properties of the

atoms including:
w Electronegativity: A measure of the ability of an
atom in a molecule to attract electrons to itself.
Hydrogen (H) 2.1 Carbon (C) 2.5

Nitrogen (N) 3.0 Oxygen (O) 3.5
Phosphate (P) 2.1 Sulfur (S) 2.5
20
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10
Biomolecule reactivity is found in functional

groups that have polar bonds.
C-O Carboxyl, Carbonyl

H-O Alcohol
H-N Amino
H-S Thiol or Sulfhydryl
P-O Phosphate, phosphoryl
21
Fall 2016
There are 5 different types of biochemical

transformation involving bond formation
or bond breakage:
1. Group transfer
2. Oxidation-Reduction
3. Rearrangement
4. Cleavage
5. Condensation
22
Fall 2016
11
Molecules with mostly C-H and C-C bonds (e.g.

Saturated hydrocarbons) - are non-polar or only
slightly polar and tend to be non-reactive.
H3C CH2 CH3
CH2 CH2
The C-O bond is polar:
+ -
C O
23
Fall 2016
Biomolecule % in E. coli
Protein 15
Nucleic Acid 7
Carbohydrate 3
Lipid 2
Water 70
Other 3
Water or H2O is of central importance to biochemistry

because it is the main solvent of the cell.
24
Fall 2016
12
Chapter 2: Water
Water or H2O is of central importance to biochemistry

because it is the main solvent of the cell.
Living organisms are largely water, with an intricate

structure of polymeric molecules compartmentalizing
the solution.
Water is a solvent for ionic and polar substances. Its

ability to ionize and participate in acid-base reactions is
fundamental to function of biomolecules, eg. proteins.
25
Fall 2016
Chapter 2: Water
The properties of water are explained by its structure

and the ability of the O to form additional bonds with
H2O and other molecules
- -

Two orbitals of O are involved
in covalent bonds with H, two
remain unbonded, each with O
an unshared electron pair. O is
more electronegative than H
creating a permanent dipole. + H 104.5 H +
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Fall 2016
13
Water and the Hydrogen bond
- -

Water exists as a Hydrogen-bonded network
with an average of 4 H-bonds per molecule in O
ice and 3.4 in liquid. -

H -
H
+
104.5
H +
O H H
In water, H-bonds H
are continually OO O
H H
being broken and H 104.5
H H
reformed, whereas +
H HO + O
H
in ice there is largely H H H
a rigid matrix. O
O
H
27
Fall 2016
H-bond: An electrostatic attraction between

polarized molecules containing O-H, N-H, or F-H.
The hydrogen bonded matrix formed by water gives
rise to its high melting and boiling points (relative to
its low molecular weight).
H2O (MW 18) CH3OH (MW 32) CH4 (MW 16)
MP 0C -98C -184C
BP 100C 65C -161C
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Fall 2016
14
H-bonds are strongest when linear i.e. the two

heavy atoms and the shared H are in a line.
H-bonding (free energy C

= 8-21 kJ/mol) is a 712 kJ / mol
O
Weak Interaction 20 kJ / mol
compared to covalent H
bonding. 389 kJ / mol
N
29
Fall 2016
Breaking H-bonds requires the addition of

enthalpy.
DHmelting = +6 kJ/mol
So why does water melt so easily at 25oC?
30
Fall 2016
15
The explanation is that the liquid is more disordered

than the solid. Recall the equation for Gibbs free
energy:
DG = DH - T DS
At 25oC: TDSmelt > DHmelt and DGmelt < 0
DGmelt = DHmelt - TDSmelt
so melting is an entropy-driven process.

31
Fall 2016
Biomolecules and the H-bond
H-bonds are not unique to water:

biomolecules interact with each other and
water via H-bonding:
AMINE
R2 ALCOHOL H
N R2 H
O H O O
R1 R3 H
O Ser O H H
KETONE
R1 H
ALDEHYDE
As a result, water will dissolve polar and

charged molecules (ie. hydrophilic molecules).
32
Fall 2016
16
Electrostatic Interactions
Electrostatic Interactions: Attraction

between oppositely charged ions - free
energy up to 50 kJ /mol
- +
Asp CH2 COO H2N C NH Arg
NH2
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Fall 2016
Electrostatic interactions
Salts such as sodium chloride (NaCl) are also easily

solubilized because waters hydrate and stabilize Na+
and Cl+ ions via Electrostatic interactions:
H2O
H H O
O H H
Na Cl Na+ + Cl-
O H H
H H O
34
Fall 2016
17
Electrostatic interactions
Electrostatic interactions: e.g. NaCl

1. When NaCl dissolves in H2O enthalpy is required to break
Na+ Cl- ionic bonds. (+DH)
2. Enthalpy is also required to disrupt H-bonding of H2O (+DH)
3. Enthalpy is also released when new water-ion interactions
form (solvation) (-DH)
4. The net enthalpy change is therefore small.
5. Solid NaCl is highly ordered. NaCl in solution is highly
disordered. So the large entropy increase favours
dissolution.
TDS >> DH and DG < 0

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Fall 2016
van der Waals Interactions
van der Waals Interaction: A short range, very

weak attraction, free energy ~ 4 kJ / mol.
w Eg. Non-polar He atoms form a liquid at 4K due to an
induced dipole attraction.
- + - +
Temporary Dipoles
36
Fall 2016
18
Non-polar hydrocarbons interact with

each other by van der Waals interactions.
CH3 CH3
CH2 CH2
CH3 CH3
37
Fall 2016
When a non-polar, hydrocarbon dissolves in water, van der

Waals (vdW) interactions and water H-bonds are broken.
New water H-bonds are formed in an organized cage
around the hydrocarbon. This optimizes the vdW
interactions between the hydrocarbon and water, and
optimizes the H-bonding among the water molecules.
But the entropy of water is reduced, disfavouring

dissolution of hydrocarbons in water.
This is called the Hydrophobic Effect.
38
Fall 2016
19
ORDERED WATER CAGE

(reduced entropy (unfavorable))
H O H
O H H
H H O O
H O H H
H H3 C H
C C H O
O H C C H H
H H H CH3
O
H
H O H H
H H O H
O
H
O
H
H
H2O entropy
maximized
HYDROPHOBIC Image reproduced from :
http://www.madsci.org/posts/archives/2004-05/1085880426.Bc.r.html
MOLECULE Author: Steve Mack
39
Fall 2016
Amphipathic molecules
Amphipathic molecules contain both polar

and non-polar groups. E.g. detergents, lipids,
proteins.
w Their lowest free energy states have hydrophobic
groups clustered together away from the water,
raising the water S.
w They help organize detergent micelles,
membranes, and proteins.
40
Fall 2016
20
A detergent: Sodium dodecyl sulfate

O
Na+ -O S O CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3
O
Hydrophilic Hydrophobic tail
Head group
w It forms a micelle in which the hydrocarbons

interact with each other via vdW forces to form a
hydrophobic core, while the hydrophilic groups
associate with water. (diagram next page) 41
Fall 2016
Micelles of fatty acids form as shown (soaps) with a

hydrophobic core and hydrophilic exterior.
w Many structures in
living organisms
including enzymes and
membranes are based on
such a structure
(diagram)
42
Fall 2016
21
Ionization of Water
- +
H2O OH + H
Keq = [H+] [OH- ] = 1.8 x 10-16 M @ 25oC
[H2O]
[H2O] = 55.5 M (moles / L)
Thus, (Keq x 55.5 M) = [H+][OH- ] = 10-14 M2 = Kw
So, 1014 1014

[H ] = OH
+
or [OH ] = H +
-
[ ] [ ]
43
Fall 2016
Ionization of Water
A convenient way to express [H+] is pH.

pH = - log10[H+]
w In pure water: [H+] = 10-7 Molar
So, - log10[10-7] = - (-7) = 7 = pH
Conversely pOH = - log10[OH-]

w In pure water - [OH-] = 10-7 Molar
So, - log10[10-7] = - (-7) = 7 = pOH
44
Fall 2016
22
Ionization of Water
When pH = pOH we have neutrality
pH can range from 0 to 14.

w Below pH 7 acidic - gastric juice is pH 1.
w Above pH 7 basic - egg white is pH 8.
pOH rarely used, pH is most common
45
Fall 2016
Strong Acids and Bases
A strong acid (complete dissociation) results in:

HCl H+ + Cl-
0.1 M 0.1 M pH = 1
0.01 M 0.01 M pH = 2
0.001 M 0.001 M pH = 3 etc.
A strong base (complete dissociation) results in:

NaOH Na+ + OH-
0.1 M 0.1M 1014 pH = 13
[H+ ] = 101
1014
0.01M 0.01M [H+ ] = 102
pH = 12
46
Fall 2016

23
Weak Acids and Bases
Most biological acids and bases are weak.

w i.e. they undergo incomplete dissociation.
O O
CH3 C CH3 C + H+
-
OH O
acetic acid acetate ion

Weak Acid Conjugate base
A weak acid is a proton donor.
47
Fall 2016
NH3+ + OH
-
NH2 + H2O
Weak base Conjugate acid
A weak base is an proton acceptor.

Biochemists choose to express all weak acids and
bases as weak acids, so:
NH3+ NH2 + H+
Weak acid conjugate base
48
Fall 2016
24
-
In general, HA A + H+
!"H + #$!"A #$ !"H + #$[ conjugate base ]
Ka = =
[ HA] [weak acid ]
This is the acid dissociation constant and commonly
expressed as :
pKa = - log10[Ka]
w The weakest acids have the largest pKas.
w E.g The pKa of acetic acid is 4.76, the pKa of
ammonia is 9.25. 49
Fall 2016
If pKa < 7.0, ionization is > H2O and therefore an ACID

If pKa > 7.0, ionization is < H2O and therefore a BASE
50
Fall 2016
25
Titration curves
Analysis of titration curves provides a better insight

into the properties of weak acids and bases:
Example 1) a strong acid mixed with a strong base:
Start with 20ml 0.1M HCl and titrate with 0.1M NaOH:
Explanation??
51
Fall 2016
Titration curves
At the start, there are 2mmol of HCl (M=moles/L ie. moles = M x L)

1. When 20ml NaOH is added, 2mmol of NaOH is
present:
NaOH reacts with HCl:
2HCl + 2NaOH 2Na+ Cl - + 2H2 O
and no acid or base is present, therefore pH 7.0.
2. When only 10ml of NaOH (1 mmol) is added:
2HCl + 1NaOH 1HCl + 1Na+ Cl - + 1H2 O
Therefore, 1mmol
[H ] =
+
30ml
= 0.033M or pH = 1.48
52

Fall 2016
26
Titration curves
Example 2) weak acid mixed with NaOH (strong base)

At the start: 20ml 0.1M (2mmol) CH3COOH and 0.1M
NaOH is added:
53
Fall 2016
Titration curves
1. at A: 20 ml 0.1M CH3COOH (2 mmol) and 10 ml 0.1M

NaOH (1 mmol) react as follows:
2CH 3COOH + 1NaOH 1CH 3COOH + 1CH 3COO - Na + + 1H 2O
(Note: before doing any calculations, always
determine what reaction takes place)
At the inflection point A, there

are equal amounts of the weak
acid and conjugate base
This is a buffer - a mixture of a
weak acid and its conjugate base
54
Fall 2016
27
Titration curves
2. At B: 20 ml 0.1M CH3COOH (2 mmol) and 20 ml 0.1M NaOH

(2 mmol).
2CH 3COOH + 2NaOH 2CH 3COO - + 2Na + + 2H 2O
Therefore, pH 7.0 because

only conjugate base present
The flat zone around 10ml
NaOH is the buffer zone
and is most effective 0.5-1 pH
units on either side of A.
We will revisit the pH at A
55
Fall 2016
Titration curves
The added OH- reacted with H+ to yield H2O. The Law

of Mass Action then causes the HA to ionize to release
more protons until the added OH- is neutralized.
-
HA A + H+
So [HA] has decreased, [A-] increased as H+
are released from HA to neutralize incoming
OH- ions. The pH eventually increases as HA
becomes less abundant.
The added OH- will neutralize an equal
number of moles of HA. 56
Fall 2016
28
Titration curves
When 10 mL of NaOH was added, the [OH-

] added = 1/2 [HA].
The acid is half neutralized and so half
dissociated [HA] = [A-]
i.e. [Weak Acid] = [Conjugate Base]
K a [HA]
[H + ] = so [H ] = K
+
a
[ ]A
And pH = pKa
57
Fall 2016
Titration curves
58
Fall 2016
29
Titration curves
Near the end of the curve, when there is no

more HA to ionize, the pH will rise
sharply.
The same graph could have been produced

by adding HCl to a solution of sodium
acetate, the conjugate base of acetic acid.
59
Fall 2016
Titration curves
Features of titration curves.

w At the ends of the curves small additions of
acid and base result in large changes in pH.
w In the middle, small additions of acid or base
cause small changes in pH. The region where
pH = pKa is called the buffering region.
60
Fall 2016
30
Buffers
A Buffer is a mixture of weak acid (WA)

and conjugate base (CB) that resists changes
in pH when small additions of acid or base
are added.
How does it work?
w Near the pKa [WA] ~ [CB], so
w The WA can neutralize added OH-, and the CB
can neutralize added H+.
61
Fall 2016
Buffers
The main buffer system found in cells is:

- - -
H2PO4 + OH HPO42 + H2O
- -
HPO42 + H+ H2PO4
The pKa of H2PO4- is 7.2.
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31
The Henderson Hasselbalch
Equation
If we know the pKa of a weak acid and the ratio

of WA to CB, we can determine the pH:
[H + ] = a A[ ]
K HA
w We first rewrite:
[ ]
in terms of pH and pKa:
pH = pK a log
[HA]
or pH = pK a + log
[ A]
-
[ A ] [HA]
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Fall 2016

Equation
pH = pK a + log
[A ]
-
[HA]
Using this Henderson-Hasselbalch Equation
we can calculate the pH of a WA-CB pair if
know their ratio and the pKa.
we
64
Fall 2016
32
Equation
WA-CB pairs buffer well as long as:

1
<
[CB] <
10
10 [WA] 1
pH = pKa + log10 [1/10] = pKa - 1.0
pH = pKa + log10 [10/1] = pKa + 1.0

For acetic acid the range is: 3.76 5.76
65
Fall 2016

Equation
Example Calculation:
What is the pH of a 20 mL solution of 0.1 M Tris
(R-NH2, pKa = 8.1) after addition of 10 mL of
0.1 M HCl (Note: R-NH2 = (HOCH2)3C-NH2)
1. First we calculate that we have 2 mmoles of
Tris and 1 mmole of HCl.
2. The reaction will be:
-
2 RNH2 + 1HCl 1 RNH2 + 1 RNH3+ + 1 Cl
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33
Equation
-
2 RNH2 + 1HCl 1 RNH2 + 1 RNH3+ + 1 Cl
So, 1 mmole of strong acid has neutralized 1 mmole
of conjugate base giving 1 mm of WA and 1 mmole
of CB
From the Henderson-Hasselbalch equation:
mmol in 30 mL] }
{[1[1mmol
pH = 8.1 + log in 30 mL]
pH = 8.1 + log 1 = 8.1

67
Fall 2016

Equation
Example Calculation #2:
Remember:
w When you add a weak acid to water, some of it
will dissociate spontaneously into its conjugate
base.
w When you add a weak base to water, some (a very
small amount) of it will spontaneously protonate
into its conjugate acid form.
68
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34
Equation
Example problem #2:
For example, Tris base, when added to water, will spontaneously
dissociate into the following:
(HOCH2)3C-NH2
H2O
(HOCH2)3C-NH2 + (HOCH2)3C-NH3+ + HO- + H2O

Tris in solution exists as an equilibrium of its weak base and conjugate
acid. If the concentration of one increases, the other decreases. This
can be accomplished by adding or removing H+ from the solution (i.e.
changing the pH). The total amount of Tris never changes, only the
relative concentrations of its acid and base forms. 69
Fall 2016

Equation
Problem:
A buffer is prepared by dissolving 0.1 mol of Tris base (pKa =
8.1) in 450 ml water, adjusting the pH to 7.8 with HCl, and
bringing the final volume to 500 ml.
RNH2 + HCl --> RNH2 + RNH3+ + Cl-
All we know is that enough HCl was added to bring to the pH to 7.8.
Question: What are the resulting amounts of RNH2 and RNH3 in 20
mls of this solution??
70
Fall 2016
35
Equation
Problem:
First we need to know the total amount of Tris in only 20mls:
0.1 mol x (20/500) = 0.004 mol (4 mmol) are in 20 mls
Let the number of mmol Tris acid = X

Then the mmol of Tris base must be = (4 - X)
From H-H equation: [conjugate base]

pH = pKa + log
[weak acid]
(4 x)
7.8 = 8.1+ log
x
71
Fall 2016

Equation
Problem:
Remember: The number of mmol Tris acid = X
so the mmol of Tris base must be = (4 - X)
(4 x)
log = 0.3
x
4x
= 10 0.3 (= 0.5)
x
72
Fall 2016
36
Equation
Problem:
4x
Now solve for X:
= 0.5
x
4 - X = 0.5X
4 = 1.5X
X = 2.66 mmol = the amount of Tris acid
Thus, the amount of Tris base is:
4 - 2.66 = 1.34 mmol
Remember: The number of mmol Tris acid = X

so the mmol of Tris base must be = (4 - X) 73
Fall 2016

Equation
Problem:
Now lets add some NaOH to the Tris solution where the initial pH
is 7.8 and we figured out that the concentrations of Tris acid is 2.66
mmol and Tris base is 1.34 mmol:
We are going to add 2 mls of 1.0 M NaOH
How many moles is this?

1.0 x (2/1000) = 2 mmol
This reacts with the Tris acid, converting it to base:

Therefore the new acid amount = 2.66 mmol - 2 mmol = 0.66
Thus the new base amount is = 1.34 mmol + 2 mmol = 3.34
74
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37
Equation
Problem:
To calculate the new pH based after the addition of the NaOH:
[weak base]
pH = pKa + log
[weak acid]
" 3.34 %
pH = 8.1+ log$ '
# 0.66 &
pH = 8.1+ log(5)
pH = 8.1+ 0.7

pH = 8.8
75
Note, the pH is indeed higher than the starting pH as expected.
Fall 2016

38

Section1 Water 16

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CHEM2360/MBIO2360

Biomolecules and an Introduction to

Instructors for CHEM 2360 and MBIO 2360

Textbook: Lehninger Principles of Biochemistry, 6th Edition by

Information about the first lab

To receive a future Lab Exemption, a student must:

1. Complete the Laboratory (practical + lab exam) with an overall

2. Complete the course (i.e. a VW is not allowed if you wish to

There is no deferred Lab Exam- No Exceptions!

NEW FOR 2016.

Four Main Groups of biomolecules:

Biochem I CHEM/MBIO 2360 covers each

Organization of the 2360 Course

Genome sequencing projects provide scientists with the parts11

What are we going to focus on?

We have about one

Cellular citizens the

Inside the cell

Bios = life (Greek)

Biosphere contains more than 106 different

Most biochemical reactions are mediated by enzymes.

Synthesis and degradation of biomolecules and other

Metabolism: Organized network of reactions

Bond strength depends on the properties of the

Hydrogen (H) 2.1 Carbon (C) 2.5

Biomolecule reactivity is found in functional

C-O Carboxyl, Carbonyl

There are 5 different types of biochemical

Molecules with mostly C-H and C-C bonds (e.g.

Water or H2O is of central importance to biochemistry

Water or H2O is of central importance to biochemistry

Living organisms are largely water, with an intricate

Water is a solvent for ionic and polar substances. Its

The properties of water are explained by its structure

Water and the Hydrogen bond

H-bond: An electrostatic attraction between

H2O (MW 18) CH3OH (MW 32) CH4 (MW 16)

BP 100C 65C -161C

H-bonds are strongest when linear i.e. the two

H-bonding (free energy C

Water and the Hydrogen bond

Breaking H-bonds requires the addition of

So why does water melt so easily at 25oC?

The explanation is that the liquid is more disordered

At 25oC: TDSmelt > DHmelt and DGmelt < 0

DGmelt = DHmelt - TDSmelt

so melting is an entropy-driven process.

Biomolecules and the H-bond

H-bonds are not unique to water:

As a result, water will dissolve polar and

Electrostatic Interactions: Attraction

Salts such as sodium chloride (NaCl) are also easily

Electrostatic interactions: e.g. NaCl

TDS >> DH and DG < 0

van der Waals Interactions

van der Waals Interaction: A short range, very

Non-polar hydrocarbons interact with

van der Waals Interactions

When a non-polar, hydrocarbon dissolves in water, van der

But the entropy of water is reduced, disfavouring

ORDERED WATER CAGE

Amphipathic molecules contain both polar

A detergent: Sodium dodecyl sulfate

w It forms a micelle in which the hydrocarbons