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BCH 2333

DGD 1 & 2 Mondays


11:30 1pm
2:30 4pm
Thao Nguyen (tnguy224@uottawa.ca)
My cave/lab/office: Marion 02
Feel free to email me with questions.
You can come to visit me as well but let me know first so I can prepare cookies.
(although not desired, you may talk to me about your questions for lab
materials)

Goal of this course

Overview of fundamental concepts in biochemistry for a strong


foundation for future study of biological system

Focus: 1) major macromolecules (amino acids, nucleic acids, lipids,


carbohydrates)
- Structure, function and metabolism of those
2) chemical properties of living systems (ie. Metabolism,
pathways etc)
- Roles of membranes and organelles in cell function
- Physical properties of water, pH and buffers
3) Enzyme kinetics and metabolic regulation

Successful students can:

Demonstrate a broad knowledge of biochemical concepts

Good biochemical vocabulary

Be able to critically review experimental evidence in the scientific literature

Expection of this course & Dr.


Shuhendler
We stress on structures this is bio-CHEMISTRY.
1.

2.

Know the basic structures of every macromolecules (YES, you will be asked to
DRAW in the exam)

Hence, know their basic chemical reactivity

Appreciate the importance of chirality in biochemistry (more relevant in amino


acids & carbohydrates)

Simple reactions & mechanisms (YES, you have to review your ORGANIC
CHEMISTRY II)

Exhibit self-regulated, autonomous learning behavior

Know the factual information presented in the lecture

Be able to synthesize those info into a logical whole the big picture

Consider biochemistry in your other courses

Discover how the concepts presented impact your health, environment & the
biological world

Open to new ways of thinking and challenge old ways of thinking

Tips to do well in this course

Live your life: eat well, play sports, jog, drink well and understand the
biochemistry behind all of these processes

Schedule saves times Develop a schedule BEFORE even begin to think


about studying

Study when you are rested, alert and have planned for it. Last minute usually
is a waste of time.

Come to class: regular class attendance is essential for success especially for
BIOCHEMSITRY

Take note: take your own note pick up the important clues in class

Form a study group: good practice for this class, your university study,
science career & future

Make diagrams, pictures, summary charts, concept maps etc

Keep up

Read the text before class if the material is new to you

Trust me Biochem is awesome


Erythropoietin

Nguyen, T (2012). A study on human erythropoietin.

The Vampire Legend


The Biosynthesis of Heme

Heme
Precursor

Derivative of glycine & succinyl-CoA

4 porphobilinogen form the porphyrin ring


Final incorporation of iron into the ring form the
heme prosthetic group
Hereditary defects in the enzyme
uroporphyrinogen III cosynthase results to
congenital erythropoietic porphyria
SYMPTOMS
Urine turns red
Skin becomes photosensitive
Teeth become fluorescent due to deposition of
strongly light-absorbing porphyrins

The biochemistry of lipids

Dynamic phospholipid remodeling is important for neuronal membrane function

Bennett, SAL et al (2013). Front. Physiol. 4:168/ doi: 10.3389/fphys.2013.00168

Hydrophobicity vs Hydrophilicity

Nonpolar molecules are hydrophobic ; Polar molecules dissolve well in


water

Exclusion of nonpolar substances by water is called hydrophobic effect

This effect is critical for the folding of proteins & self-assembly of biological
membranes

Molecules that are both, are amphipathic

When a sufficiently high concentration of amphipathic compounds is


dispersed in water, they form micelles

Hydrophobicity vs Hydrophilicity

To predict hydrophilicity, look at:


1. The presence of ions
2. The presence of a dipole moment

3. The presence of London dispersion forces (van der Waals


attractive force)

Points to note:

Ions are easy for water to solvate around because they are charged

Polar = dipole moments

Substances that lack ions or dipole moment are hydrophobic. But


uncharged, nonpolar gases can still exhibit London forces. London
forces are larger as the size of the atom or molecule increases.
Molecules with greater London forces are more hydrophilic.

Hydrophilicity is the determination factor of solubility

Why is water a good solvent ?


1.

Water molecules are polar dissolve ionic & polar substances


easily

2.

Water viscosity does not impede movement of dissolve molecule


(Important in cellular concentrations and diffusion)

3.

Water molecules are small relative to other solvents, allowing


them to associate with many solute particles to increase it
solubility (Osmotic Pressure)

Physical properties of water make it an excellent solvent.

Summary of week 1 - Water


1.

Because of the uneven distribution of charge in O-H bonds and their angled
arrangement, the water molecule has a permanent dipole

2.

Water molecules can form hydrogen bonds with each other. Hydrogen bonding
contributes to the high specific heat and heat of vaporization of water

3.

Because it is polar, water can dissolve crystalline electrolytes. Water molecules form
a solvation sphere around each dissolved ion. Organic molecules may be soluble in
water if they contain ionic or polar functional groups that can form hydrogen bonds
with water molecules.

4.

Hydrophobic effect is the exclusion of non-polar substances by water molecules.


Eg. Detergents contain both hydrophobic and hydrophilic portions, form micelles
when suspended in water; these micelles can trap insoluble substances in a
hydrophobic interior. Chaotropes enhance the solubility of nonpolar compounds in
water.

Summary of week 2 - Bonds


1.

The major noncovalent interactions that determine the structure and function of biomolecules are
electrostatic interactions and hydrophobic interactions.

2.

Electrostatic interactions include charge-charge interactions, hydrogen bonds, and van der
Waals forces.
Hydrophobic interactions: dissociation energy depends on the increased entropy of surrounding
water molecules rather than on direct attraction between nonpolar groups.

3.

Under cellular conditions, macromolecules do not spontaneously hydrolyze, despite the presence of
high concentration of water.
Specific enzymes catalyze their hydrolysis and other enzymes catalyze their energy-requiring
synthesis.

4.

van der Waals forces (London dispersion force) are much weaker than hydrogen bonds (0.4 to
4kJ/mol versus 2 to 20 kJ/mol)

5.

Covalent bond has dissociation energy of approximately 340 450 kJ/mol (C-H or C-C)

In preparation for this week


content
Review your acid/base chemistry the most important chemistry in biochemistry

If you like biochemistry, you must know the chemistry in that word. And acid/base is
the utmost importance.

Prelude

At 25oC, [H+][OH-] has a value of 1.0 x 10-14 M2 = Kw the ion-product constant for water

(This means pure water ionizes to produce 10-7 M of H+ and 10-7 M of OH- )

The acidity and basicity of an aqueous solution depends on the concentration of H + and is
described by a pH value.

The strength of a weak acid is indicated by its pKa value. The Henderson- Hasselbalch
equation defines the pH of a solution of weak acid in terms of the pKa and the
concentration of the weak acid and its conjugate base.

Buffered solutions resist changes in pH. In human blood, a constant pH of 7.4 is


maintained by the carbon dioxide-carbonic acid-bicarbonate buffer system.

DGD wednesdays

eyy074@uottawa??

Memorizing aas
Part 1: https://www.youtube.com/watch?v=gq-rWb0fmzQ

Part 2: https://www.youtube.com/watch?v=C2GfoGXfySQ

Know pkas

KNOW HOW TO DERIVE THE HENDERSON HASSLEBACH eqn.

HW Q: RNA world hypothesis


provides further detail as to the
early evolution of primoridal life

Answer a) In early organisms and proto-organisms, RNA was the


predominant biomolecule responsible for both information
storage and chemical catalysis

Q: Rank from lowest to highest


dissociation constant a PH of 2. To
rank items as equivalent, overlap
them.

Lysine will be protonate**d/unprotonated? @ a PH of 2

Asparatic acid will be protonated** / unprotonated? @ pH of 2

What are favourable and unfavourable interactions?

Kd will be high