Option B
Topics B1 and B2
IB Chemistry
Mr. Thomson
AISB
Syllabus Statements
B.1.1 Calculate the energy value of a food from
enthalpy of combustion data.
Calorimetry
The heat content (Calorie content) of foods can be
determined by burning the food in a Calorimeter.
Heat produced = heat absorbed by water + heat absorbed by the Calorimeter
Calorimetry, cont.
http://chemistry.umeche.maine.edu/~amar/fall2009/bomb.jpg
Sample Problem
Solve the sample problem…
Source: IB Chemistry by Green and Damji, 2007.
Sample Problem
Heat produced = (m x c x T)water + (c x T)calorimeter
= (200 g x 4.18 J g-1 °C-1 x 45.3 °C) + (89.1 J °C-1 x 45.3 °C)
= (37871) + (4036) J
= 41907 J
= 41.9 kJ (produced by 15.0 g of apple)
Thus the energy value of the 150 g apple is 419 kJ.
Source: IB Chemistry by Green and Damji, 2007.
Syllabus Statements
B.2.1 Draw the general formula of 2-amino acids.
2-amino acids
•Have amino (NH2) group on carbon next to the
carboxyl group (COOH)
•Ex:
Structure of 2-amino acids (α-amino acids)
Source: IB Chemistry by Green and Damji, 2007.
Syllabus Statements
B.2.2
Describe the characteristic properties of
2-amino acids
Teacher notes: Properties should include isoelectric
point, formation of a zwitterion and buffer
action.
Properties of Amino Acids
•Colorless, crystalline solids.
•Exist as zwitterions (dipolar ions) with fairly high
melting points for an organic compound
•Generally soluble in water
•Amphoteric (have –NH2: basic; -COOH: acidic)
– Can act as a buffer (substance that resists changes in pH
when a small amount of acid or base is added)
Zwitterion
http://www.hcc.mnscu.edu/chem/V.27/zwitterion.jpg
How they buffer
• In solutions they form zwitterions
• When an acid is added the zwitterion accepts an H+
Buffering a Base
• When a base is added the zwitterion donates an H+
Isoelectric Point (pI)
• pH where positive and negative charges
are equal
• No net charge
• No migration in electric field
Basic and Acidic Acids
• If # of NH2 groups > COOH acid is basic
• If # of NH2 groups < COOH acid is acidic
• The pH determines the charge on the
Amino Acid
• This makes them move in electric fields
• Electrophoresis – will come back to this
Look at Table 19 and find an acidic and a
basic amino acid.
http://www.detectingdesign.com/i
mages/Abiogenesis/Amino%20Aci
d%20Chart.jpg
Syllabus Statements
B.2.3
Describe the condensation reaction of
2-amino acids to form polypeptides.
Teacher Notes:
Reactions involving up to three amino acids
will be assessed.
Two different dipeptides
Peptide Bond
Syllabus Statements
B.2.4
Describe and explain the primary, secondary
(α-helix and β-pleated sheets), tertiary and
quaternary structure of proteins.
Teacher Notes:
Include all bonds and interactions (both
intramolecular and intermolecular)
responsible for the protein structure.
Primary Structure of Proteins
•Order of amino acids forming proteins
•Indicated by 3-letter code for amino acid
•Ex: tripeptide made of lysine, glutamine, and
leucine = lys-gln-leu
•leu-gln-lys is a different tripeptide
•Each protein has a different sequence which allows
it to have a different function
Primary Structure
The amino acid sequence.
Source: IB Chemistry by Green and Damji, 2007.
Secondary Structure
• Way a polypeptide chain folds or aligns
itself in certain repeating patterns
• Arrangement in space of polypeptide chain
• Usually an α-helix or β-pleated sheet
α-helix
Source: IB Chemistry by Green and Damji, 2007.
β-Pleated sheet
Folded so that
chains face
opposite of each
other
β-pleated sheet
Source: http://www.nd.edu/~aseriann/bstr2.gif
Tertiary Structure
• How a protein folds to form the globular
structure.
Tertiary Structure
Source: IB Chemistry by Green and Damji, 2007.
Tertiary Structure 3D
Secondary
structure
twists and folds
to form 3D
shape
RCSB Protein Data Bank.
Stability of Tertiary Structure
Disulfide bridge
formed from
adjacent cysteines
3D stability – H bonding
On side chains (R)
between polar
groups
3D stability – ionic bonds
Side chain (R)
can have groups
that allow for
formation of
zwitterions which can
bond
Hydrophobic Interactions/Folding
• Folding of the protein such that the nonpolar (hydrophobic) side groups tend to
clump together on the inside of the protein,
forcing the protein into a specific tertiary
structure with the polar parts of the
molecule on the outside.
• Water is excluded from the non-polar
interior of the protein.
Quaternary
• Only for polypeptide chains held together by
hydrophobic interactions, H-bonds and/or ionic
bonds
• Each polypeptide chain called a subunit
• The way subunits are held together in a precise
structural arrangement is 40
• Ex: hemoglobin- four poly-peptide chains, each
of which is bound to a heme group. The two α
chains and the two β chains are identical.
Hemoglobin
http://www.mun.ca/biology/scarr/MGA2-03-26b.jpg
• http://www.stolaf.edu/people/giannini/flash
animat/proteins/protein%20structure.swf
Summary of structure
• 10 – order of a.a. - set of three a.a. abbreviations
• 20 – arrangement in space of polypeptide chain
- α- helix or β- pleated
- held together by H-bonds. Between?
• 30 – 3D shape - held together by:
- covalent bonds – disulfide bridge
- H bonds – polar groups on side chain
- ionic bonds (salt bridge) – side chains of
ions (NH3+ and COO-)
40 – Subunits joined – only for molecules with 30
held together by H bonds or ionic bonds
Syllabus Statements
B.2.5
Explain how proteins can be analysed by
chromatography and electrophoresis.
Denaturing
•3D structure can be lost and with it biological
function
•Heat, ionizing radiation
•pH, salt concentrations – disrupt ionic bonds
•Organic solvents and detergents – disrupt
hydrophobic interactions
•Hg and Pb poisoning due to disruption of disulfide
bridges
Hydrolyzing Peptide Bonds
•peptide bonds are strong due to resonance
•Conditions to hydrolyze:
– 6M HCl
– 1100C for 1-3 days
•Produces individual amino acids
Protein Analysis
•Hydrolyze or “undo” peptide bond in a protein
allows the a.a. composition to be analyzed
Electrophoresis
•Method of separating molecules on the basis of
their electric charges
•First hydrolyze protein to break peptide bonds and
release amino acids. Conditions?
•Acidic and basic side chains produce + and – ions in
amino acids
•Number of ions affects behavior in electric field
•# of ions affected by pH
Set-up
• Electrolyte solution
buffered to a certain pH
• Paper saturated with
solution
Charge vs. movement
•If amino acid is at pI – doesn’t move (neutral)
•If amino acid + moves toward cathode (negative)
•Amino acid is + if buffer is more acidic (acidic buffer
will turn O- in OH leaving +)
•If amino acid – moves toward anode (positive)
•Amino acid is – if buffer is more basic (basic buffer
will take H+ from NH3+ leaving -)
•Faster the migration, larger difference between pI
and pH
Analysis
•When a.a. separated, sprayed with ninhydrin – to
see (like on CSI)
•Paper compared with known pI to identify amino
acid
Example: Remember it’s all about the buffer!
•Glycine
H3N+-CH2-COOpI = 6
•At pH = 6 ions equal, no movement
•At pH = 7, buffer more basic than pI so get H2N-CH2-COOnet charge is negative, so move toward positive electrode
(anode)
•Above pI – a.a. negative
•At pH = 5, buffer more acidic than pI, so get H3N+-CH2COOH net charge is positive so move toward cathode
(negative)
•Below pI – amino acid positive
Practice
• Where would each of the following end up
relative to each other in pH =6?
• Cystine, Glutamine, Glycine, Histidine,
Lysine
+
-
Cathode
•
Lys
Anode
His
Gly
Gln
Cys
Chromatography
• Separation technique based on solubility
• Amino acids are hydrophilic so paper
chromatography works well to separate
• Stationary phase - H2O adsorbed into paper
• Mobile phase – eluting solvent (1-butanol and
ethanoic acid)
• Solvent flows through paper by capillary action
• Solute (a.a.) partitioned between 2 solvents –
H2O (stationary) and eluting solvent (mobile)
Movement
• If a.a is more strongly attracted to the
water that is adsorbed into paper – doesn’t
move
• If a.a. is more strongly attracted to eluting
solvent (1-butanol and ethanoic acid) –
moves
Chromatography setup
Source: IB Chemistry by Green and Damji, 2007.
Setup
Reading chromatogram
• Components of mixture move relative to
solubility in two phases
• When solvent near top of paper, remove
and spray with ninhydrin (pretend you are
on CSI)
• Spots formed in different places
• Identity of a.a. from Rf value of spots
compared to known Rf value of a.a.
Rf Value
Source: IB Chemistry by Green and Damji, 2007.
Syllabus Statements
B.2.6
List the major functions of proteins in the
body.
Teacher Notes:
Include structural proteins (for example,
collagen), enzymes, hormones (for example,
insulin), immunoproteins (antibodies),
transport proteins (for example, hemoglobin)
and as an energy source.
Functions of Proteins
•Structural proteins (collagen: skin; keratin: hair)
•Enzymes
•Hormones (insulin)
•Immunoproteins (antibodies, interferons)
•Transport proteins (hemoglobin)
•Energy source
What you should do now?
Practice problems, with Markscheme (to be?) posted
on Moodle.