Welcome to Bio 98B

Biochemistry
Professors: Hartmut “Hudel” Luecke & Markus Ribbe

Discussion section leaders:

Anais Sahabian sahabiaa@uci.edu (1)
Mariana Remedios-Chan remediom@uci.edu (2)
Maribel Arias maribela@uci.edu (3)

Elyse Paterson epaterso@uci.edu

Iris Kim irisk@uci.edu
Jared Wiig jwiig@uci.edu

© 1998-2011, unauthorized or for-profit use strictly prohibited.

Hartmut “Hudel” Luecke

Department of Molecular Biology & Biochemistry

Area of research: Structure & function of proteins

Office Hours: Make appointment via email

Email: hudel@uci.edu (Please put “bio98” in subject line of all emails)
• Class web site: http://bass.bio.uci.edu/~hudel/bs98a/index.html
• Assigned reading and problems
• Discussion sections - start next Monday!
• How to do well in this course:
assigned reading - before the lecture
lectures - attend
problems - try/read/try again
discussion sections - go prepared
 Bio 98 Tutoring
Bio 98B TAs:
•  Anais Sahabian sahabiaa@uci.edu (1)
•  Mariana Remedios-Chan remediom@uci.edu (2)
•  Maribel Arias maribela@uci.edu (3)

•  Elyse Paterson epaterso@uci.edu

•  Iris Kim irisk@uci.edu
•  Jared Wiig jwiig@uci.edu

UCI Bio Sci Peer Tutoring:

https://eee.uci.edu/programs/biotutor

LARC Tutoring: http://www.larc.uci.edu/

 Biochemistry

Physics Chemistry

Biology
Central Dogma of Biology

replication!
DNA (4 bases: dA, dT, dG, dC)!

transcription!

RNA! (4 bases: A, U, G, C)!

translation!

PROTEIN (20 amino acids)!

 PROTEINS!

• enzymes – catalyze chemical reactions

• transport – move molecules
• receptors – transduce signals
• structural proteins – architecture of cells

Bio 98: Structure & function of proteins; metabolic

reactions, lipids and carbohydrates.

Bio 99: Informational macromolecules: DNA and RNA,

replication, transcription & translation.
 Outline of Today’s Lecture

I. !Structure and properties of water!

A. Life depends on water
B. Unusual and important properties of water

II. !Biochemical forces!

!A. Strong vs. weak forces (bonds)
B. Non-covalent forces: general features
C. Four types of non-covalent interactions
I. !STRUCTURE AND PROPERTIES OF WATER!

No water = No life

Most living organisms contain about 70% water

I. !STRUCTURE AND PROPERTIES OF WATER!

Oceans hold 97% of surface water, glaciers

and polar icecaps 2%, ground water and land
surface water such as lakes & rivers 1%.

I. !STRUCTURE AND PROPERTIES OF WATER!

B.  Unusual and important properties of water:

1. Water is the only substance on Earth that exists
in all three physical states of matter.
2. High boiling & melting points for such a small
molecule; compare water with methanol (mass
of 18 vs. 32 Dalton).
3. Density of liquid water > density of ice.
4. Very polar - metabolites and ions are soluble
- but lipids are not.
I. !STRUCTURE AND PROPERTIES OF WATER!

B.  Unusual and important properties of water:

1. Water is the only substance on Earth that
naturally exists in all three physical states of
matter: solid, liquid and gas
I. !STRUCTURE AND PROPERTIES OF WATER!

B.  Unusual and important properties of water:

3. Density of liquid water > density of ice.
When water freezes it expands rapidly, increasing
about 9% in volume. Fresh water has a maximum
density at 4 °Celsius. Water is the only substance
where the maximum density does not occur when
solidified. As ice is less dense than liquid water, ice
floats on water.

What would happen if ice didn’t float?

I. !STRUCTURE AND PROPERTIES OF WATER!

Density of liquid water

I. !STRUCTURE AND PROPERTIES OF WATER!
1. Oxygen has 6 valence electrons
2. Uses bonds to H atoms to fill valence shell (8)
3. Large dipole
4. Can form extensive H-bonding network
(donate 2 and accept 2 H-bonds per water)
 Dipoles

δ +
H
δ- O
H δ+
Arrow indicates direction of dipole.
The greater the charge separation, and
the greater the (partial) charges, the
greater the dipole moment.

 Polar molecules and dipoles

δ+ C O δ- C O Net dipole

δ-
N N
Net dipole
H H H H
δ + H + H
δ
δ+

δ+
δ- O=C=O δ- O=C=O No net dipole
 Hydrogen bonding

~2.8 Å ~1.8 Å / ~0.18 nm

~0.28 nm

1 Å / 0.1 nm

Typical strength of a water-water hydrogen bond: ΔH = -20 kJ mol-1

Structure of ice
Dissolution of sodium chloride
 Dissolution of sodium chloride

Movie: Water dissolves table salt (NaCl):

http://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/molvie1.swf
What happens to a hydrophobic molecule in water?
Hydrophilic: water “loving”
Hydrophobic: water “fearing”

1. Aliphatic side chain disrupts water

structure
2. Water cannot H-bond with hydrocarbon
3. Water must order itself around the
hydrocarbon without optimal H-bonds.
Such ordering is entropically not favorable.
4. Energetically more favorable for
hydrocarbon to separate from water. That’s
why oil and water don’t mix.
Movie: Hydrophobic hydration of xenon:
http://www.rpi.edu/~paschd3/movies.html
Detergents & micelles polar head group

hydrocarbon tail

O
- Na +
H3C (CH2)11
4 S O
O transfer to water

polar groups point out toward water

Sodium dodecyl sulfate (SDS),

an amphipathic molecule

amphi = 2 sides
pathic = coming together
II. !BIOCHEMICAL FORCES!
A. Strong vs. weak forces
1. covalent bonds: strong, 200-800 kJ/mol
2. non-covalent bonds: relatively weak,
0.4-200 kJ/mol

calories and joules – units of energy

calorie (chemistry): 1 cal = energy required to raise temperature of
1 gm water by 1.0 °C.
Calorie (dietetics): 1 Cal = 1,000 calories = 1 kcal

Joule (physics): 1 J = 0.239 cal and 1 cal = 4.18 J

1 kJ = 1,000 J = 239 cal = 0.239 kcal
B. Non-covalent interactions
(of special importance in biology)

Easily changed or modified, more dynamic

than covalent bonds. Examples:
• base pairing of DNA double helix
• RNA-DNA interactions in transcription
• folding of proteins
• binding of metabolites to enzymes
Four types of non-covalent interactions

1. Charge-charge (ionic) interactions

• non-directional
• distance-dependent (1 / r2)
• attractive or repulsive
• energy: 40-200 kJ mol-1

O
+
C + Na
H3C O NH3
CH3 Cl
 Four types of non-covalent interactions

2. Hydrogen bonds R1 δ- +δ R3
• highly directional C O H N
• fixed length (2.4 – 3.2 Å)
R2 R4

Donors: R-NH, R-OH, R-SH

Acceptors: :O: or N: via unshared pair of electrons

Most H-bonds require 2-7.5 kJ mol-1 to break and are thus

weaker than those between water molecules.
Angular dependence of H-bond strength
3.  Van der Waals forces

• due to permanent, transient or induced

dipoles that occur in all molecules

• weakest of the non-covalent forces

(between 0.4 – 4 kJ mol-1)
For carbon atoms the
optimal distance for stability
is about
3 Å = 0.3 nm = 3 x 10-8 cm.

In contrast, the distance of a

typical covalent C-C bond is
1.5 Å.
4. Hydrophobic interaction
• coalescence of non-polar, “water-fearing”
molecules in an aqueous environment
• force of coalescence provided mainly by
stability of the H-bonding network of
surrounding water - very little by the
inherent attraction of the non-polar
molecules to each other
• hydrophobic interactions are stronger than
Van der Waals forces: 3-10 kJ mol-1
 Midterm Exam

reading problems

lectures

-  short answers, diagrams, calculations

-  fact sheets provided: Table 3-1, Fig. 3-5
-  pKa values provided where needed
-  previous exams available on website