Welcome to 3FF3! Bio-organic Chemistry. Jan. 7, 2008. Instructor: Adrienne Pedrech ABB 417 Email: [email protected] -Course website: http://www.chemistry.mcmaster.ca/courses/3f03/index.html Lectures: MW 8:30 F 10:30 (CNH/B107)
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Jan. 7, 2008
-Course website: http://www.chemistry.mcmaster.ca/courses/3f03/index.html
Lectures: MW 8:30 F 10:30 (CNH/B107)
2:30-5:30 M (ABB 302,306) **Note: course timetable says ABB217 2:30-5:30 F (ABB 306)
For Monday 7th & Friday 11th
Assignments 2 x 5% 10%
Labs: -write up 15%
- practical mark 5%
Fri. Feb. 29, 2008 at 7:00 pm
Make-up test: TBD
Assignments: Feb.6 – Feb.13
Mar.7 – Mar.14
Note: academic dishonesty statement on outline-NO copying on assignments or labs (exception when sharing results)
Background & “Refreshers”
This course has selected examples from a variety of sources, including Dobson &:
“Development & use of chemistry techniques for the study of biological phenomena” (Stuart Schreiber)
“Understanding how biological processes are controlled by underlying chemical principles” (Buckberry & Teasdale)
“Application of the tools of chemistry to the understanding of biochemical processes” (Dugas)
What’s the difference between these???
Deal with interface of biology & chemistry
Simple organics bio?
eg HCN, H2C=O
large macromolecules; cells—contain ~ 100, 000 different compounds interacting
Biologically relevant organics: polyfunctional
1 ° Metabolism – present in all cell (focus of 3FF3)
2 ° Metabolism – specific species, eg. Caffeine (focus of 4DD3)
How different are they?
Exchange of ideas: bio?
Bases + sugars → nucleosides nucleic acids
Sugars (monosaccharides) polysaccharides
Amino acids proteins
Polymerization reactions; cell also needs the reverse process
We will look at each of these 3 parts:
for structural prediction (e.g. protein folding)
2) Size → multiple FG’s (active site) ALIGNED to achieve a goal
(e.g. enzyme active site, bases in NAs)
3) Multiple non-covalent weak interactions → sum to strong, stable binding non-covalent complexes
(e.g. substrate, inhibitor, DNA)
4) Specificity → specific interactions between 2 molecules in an ensemble within the cell
5) Regulated → switchable, allows control of cell → activation/inhibiton
6) Catalysis → groups work in concert
7) Replication → turnover
e.g. an enzyme has many turnovers, nucleic acids replicates
In this course, we will follow some of the ideas of how life may have evolved:
Which came first: nucleic acids or protein?
RNA world hypothesis suggests RNA was first molecule to act as both template & catalyst:
catalysis & replication
How did these reactions occur in the pre-RNA world? In the RNA world? & in modern organisms?
CATALYSIS & SPECIFICITY
How are these achieved? (Role of NON-COVALENT forces– BINDING)
a) in chemical synthesis
b) in vivo – how is the cell CONTROLLED?
c) in chemical models – can we design better chemistry through understanding biochemical mechanisms?
All of these demonstrate inter-disciplinary area between chemistry & biology
Two Views of DNA RNA world? & in modern organisms?
Biochemist’s View of the DNA Double Helix RNA world? & in modern organisms?
Chemist’s View RNA world? & in modern organisms?
6 RNA world? & in modern organisms?π electrons, stable cation weaker acid, higher pKa (~ 5) & strong conj. base
sp3 hybridized N, NOT aromatic strong acid, low pKa (~ -4) & weak conj. base
Forms supramolecular structure: 6 molecules in a ring
Create new architecture by thinking about biology i.e., biologically inspired chemistry!
** Try these mechanisms!
electical discharge neutral!
CH4 + N2 + H2
This is an SN2 reaction with stereospecificity
Also see Dobson, ch.9
Topics in Current Chemistry, v 259, p 29-68
The last structure is the Fischer projection:
& its enantiomer is: (S)-L-(-)-l-glyderaldehyde
(+)/d & (-)/l do NOT correlate
D/L erythrose – pair of enantiomers
D/L threose - pair of enantiomers
“reducing sugars” – those that have a free aldehyde (most aldehydes) give a positive Tollen’s test (silver mirror)
Why do we get cyclic acetals of sugars? (Glucose in open form is << 1%)
** significant –ve ΔS! ΔG = ΔH - TΔS
Favored for hemiacetal
Not too bad for cyclic acetal
In solution, with acid present (catalytic), get MUTAROTATION: not via the aldehyde, but oxonium ion
O lone pair is antiperiplanar to C-O σ bond GOOD orbital overlap (not the case with the β-anomer)