Transcript bio98a_l01

Welcome to Bio 98
Biochemistry
Physics
Chemistry
Biology
Professors: Hartmut “Hudel” Luecke & Yilin Hu
© 1998-2015, 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: [email protected] (Please put “bio98” in subject line of all emails)
• Class web sites:
https://eee.uci.edu/15w/05350
http://urei.bio.uci.edu/~hudel/bs98a/index.html
• How to do well in this course:
Assigned reading – before each lecture
Lectures – attend!!!
Problems – try / read / try again
Discussion sections – go prepared!
Discussion sections & tutoring
Bio 98 TAs (Luecke part)
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•
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Section 1 (Alborz Karimzadeh, [email protected]): week of Jan 12
Section 2 (Rutav Mehta, [email protected]): week of Jan 26
Section 3 (Luke Nelson, [email protected]): week of Feb 2
UCI Bio Sci Peer Tutoring
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Allen Khai ([email protected])
Nobel Nguyen ([email protected])
LARC Tutoring
•
Allen Tran ([email protected])
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John Ngo ([email protected])
Biochemistry
Physics
Chemistry
Biology
Biochemistry
Biochemistry
ATP
http://en.wikipedia.org/wiki/Adenosine_triphosphate
Metabolic processes that use ATP as an energy source convert it back
into its precursors. ATP is therefore continuously recycled in
organisms: the human body, which on average contains only 250
grams (8.8 oz) of ATP, turns over its own body weight in ATP each
day.
ATP
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 that exists
in all three physical states of matter on earth.
2. High boiling & melting points for such a small
molecule; compare water with ethanol (mass
of 18 vs. 46 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 that
naturally exists in all three physical states of
matter on earth: solid, liquid and gas
I.
STRUCTURE AND PROPERTIES OF WATER
B. Unusual and important properties of water:
2. High boiling & melting points for such a small
molecule; compare water with ethanol (mass
of 18 vs. 46 Dalton).
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. Pure 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.
I.
STRUCTURE AND PROPERTIES OF WATER
B. Unusual and important properties of water:
3. Density of liquid water > density of ice.
What would happen if ice did not float on water?
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 moment
4. Can form extensive H-bonding network
(donate 2 and accept 2 H-bonds per water)
Dipoles
+
d
H
d- O
H d+
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
d+ C
O d-
C
dN
d
H
+
H
H
+
d
d+
d+
d- O=C=O d-
O
N
H
H
H
O=C=O
Net dipole
Net dipole
No net dipole
Hydrogen bonding
~2.8 Å
~0.28 nm
~1.8 Å / ~0.18 nm
1 Å / 0.1 nm
Typical strength of a water-water hydrogen bond: DH = -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 unfavorable.
4. It is energetically more favorable for
hydrocarbon to separate from water. That
is why oil and water don’t mix!

Detergents & micelles
O
H3C (CH2)11
4
S
O
- Na +
O
Sodium dodecyl sulfate (SDS),
an amphipathic molecule
amphi = 2 sides
pathic = coming together
II. (BIO)CHEMICAL 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 = 0.239 Cal
2. Non-covalent interactions
(of special importance in biology)
Easily changed or modified, thus more
dynamic and transient than covalent bonds.
Examples:
• base pairing of DNA double helix
• RNA-DNA interactions during
transcription
• folding of proteins
• binding of substrates to enzymes
Four types of non-covalent interactions
1.
2.
3.
4.
kJ / mol
Charge-charge (ionic) interactions 40-200
Hydrogen bonds
2-20
Hydrophobic interaction
3-10
Van der Waals forces
0.4-4
Four types of non-covalent interactions
1. Charge-charge (ionic) interactions
• non-directional yet long-range
• distance-dependent (1 / r)
• attractive or repulsive
• energy: 40-200 kJ mol-1
H3C
O
C
O
+
NH3
CH3
Na
+
Cl
Four types of non-covalent interactions
2. Hydrogen bonds
• highly directional
• fixed length (2.4 – 3.2 Å)
Donors:
Acceptors:
R1
d-
C O
R2
+d
R3
H N
R4
R-NH, R-OH, R-SH
:O: or N: via unshared pair of electrons
Most H-bonds in proteins require 2-7.5 kJ mol-1 to break and are
thus weaker than those between water molecules.
Angular dependence of H-bond strength
180º
120º
3. Hydrophobic interaction
• coalescence of non-polar, “water-fearing”
molecules in an aqueous environment
• force of coalescence provided mainly by
energetics 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
4. Van der Waals (VdW) 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 VdW
interaction 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.
Midterm Exam
reading
problems
LECTURES
- short answers, diagrams, calculations
- pKa values provided where needed
- previous exams available on website