bioorganic chem

8/12/2019 Bioorganic Chem

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What is Life:

A chemical system capable of Darwinian evolution(The NASA Panel, 1994)

Charles Darwin: Survival of the fittest under selectivepressure.

cf) Being alive: An individual male rabbit (for example)that is alive cannot (alone) support Darwinian evolution,

and therefore is not life.


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What Constitutes Life?(Living vsthe Inanimate)

Chemical complexity and organization- not just simplecomponentsExtract, transform and use energyfrom environment storage molecules

Self-replication and assemblygenetic material contains all information

Adaptationmechanisms to sense/respond toenvironment

Functions of components are defined and regulatedA history of evolutionary change diversity

All organisms share great similarity (cell, chemistry)

- common rules on how they function, but many exceptions


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[2] Cellular Foundations

The Cell: structural and functional units of all living organisms

Prokaryotes(Pro- before): (eu- and archaebacteria)- bacteria

- lack membrane-enclosed nucleus (= karyon)- simple structuresunicellular, filaments or colonies- cell wall (polysaccharides, peptidoglycans)- cell membrane (lipid bilayer with protein)

- cytoplasm (enzymes, proteins, many RNA species) cytosol- one or more copy of chromosome in condensed form(nucleoid)


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Eukaryotes(Eu- good or true)

- large range of species

- membrane-enclosed nucleus encapsulating DNA- unicellular or multicellular- more complex than prokaryotes 5~10 times larger- cell membrane (lipid bilayer with proteins)

- cytoplasm (enzymes, proteins, many RNA species,organelles, cytoskeleton)- 100~1000 times more DNA than prokaryotes

cell size: animal and plant cells: 5~100 m in dbacteria: 1~2 m long

Lower limitminimum number of molecules for life

Upper limitratio of surface area to vol.


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Superkingdoms Domains


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[3] The Cell Structures- Bacteria

* plasmids


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(1) Cell Membrane and Wall

Cell (Plasma) Membrane:- contains transporters, signal receptors- engulfs particles by endo-, phago- and exocytosis

(prokaryotes limited to absorption of nutrients)

Cell Wall:- plants also have a cell wall (cellulose, and other

carbohydrate polymers)


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(2) The Nucleus

(starting point for growth or development, kernel of a cell) has a a nuclear envelope (lipid/protein) and holds the majority

of the cells DNA. storage of genetic information as chromosomes.

chromosomes consist of chromatin fibers made of nucleosomes(DNA + histones). DNA information transcribed into RNA. Nuclear Envelope - double membrane bilayer, perforated with

many pores (900) to allow passage of macromolecules

(enzymes in; RNA out). Nucleolus - site of ribosomal assembly (exported to cytosol),

contains chromosomal segments encoding ribosomal RNA.


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(3) Cytosol(cytoplasm; cytocell; plasmaliquid part)water based

includes macromoleculesexcludes membrane-bound organelles

(4) Endoplasmic Reticulum & Golgi Apparatus(endowithin; plasmaliquid part; reticulumnetwork)

most extensive membrane in cellrough ER: ribosome studded, protein synthesissmooth ER: no ribosomes, lipid synthesisproducts of ER transported to Golgi apparatus for further

processingproteins addressedGolgi: stack of flattened membraneous sacs


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(5) Mitochondria(mitosthread, chondrosgranule)

evolved from aerobic bacteriasite of cellular respiration (aerobic metabolism)

large ellipsoid ~ 2000/eukaryotic cell (~ 1/5 cell)

two lipid membranes

smooth outer & highly folded inner with invaginations called cristae

has two spaces (inner membrane space & matrix internal space)

reproduce by fission (like bacteria) only from other mitochondria

respiratory enzymes form gel-like matrix of inner membrane

couples chemical energy from nutrient oxidation to synthesis

of ATP (energy storage molecule)ATP is exported to rest of cell to fuel processes

contains DNA, RNA and ribosomes for the synthesis of

some mitochondrial components


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(6) Lysosomes(lysiscut)

- single membrane, variable size- membraneous sacs containing a large variety of low pH hydrolytic

enzymes

- plants contain the analogous vacuoles

(7) Cytoskeleton(cytosolic skeleton) (Fig 1-9, p.9)- organizes, adds structure to the cytosol

- extensive array of filaments (actin, intermediate) and microtubules

(that make upcentrioles)

- gives cell shape and ability to move- orchestrates internal motion of organelles


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[4] Structural hierarchy in the molecular organization of cells

Hold by noncovalent interactions


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[5] Chemical Foundations

(1) Chemical Elements: ~30 elements are essential for life.H, C, N, O 99% of total mass.

(2) Why carbon (>50% of the total mass) ?Organic chemistry: the chemistry of carbon-containing compounds

(initially from living organisms.)

Ability to to form stable bonds (CC single bond, 83 kcal/mol)Bonding versatility:

can form single, double, triple bonds with other atoms, H, O, N, S.

can form molecules of different sizes and shapes.

Electron configuration: 1s22s22p2 4 valence electrons.

Forms hybrid orbitals

Foursp3hybrid orbitals for 4 single (, sigma) bonds in CH4.

Threesp2hybrid orbitals for 3 bonds, and 1porbital for bond.

Twosphybrid orbitals for 2 bonds, and 2porbital for 2 bonds.


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(3) Functional GroupsChemical personality (property) of a compound is determined by

the chemistry of its functional groups and their deposition in 3D space.


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(4) Molecule, mass, mole, molarity

Molecule:An aggregate of a few atoms that is the fundamentalbuilding block of matters, held together by covalent bondsbetween the atoms.

Molecular mass:Mass of a molecule in Daltons (Da).

One Da is equivalent to one-twelfth the mass of carbon-12 (12C).

The molecular mass of H2O is 18 Da.

Molecular weight(Mr, Relative molecular mass):

The ratioof the mass of a molecule to one-twelfth the mass of12C.

Dimensionless.

The molecular weight of H2O is 18.


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Mole (mol):A collection of 6.022 1023items.

Molar mass:The mass of one mole of a substance.

(= molecular mass 6.0221023)

The molar mass of H2O is 18 grams.

Molarity (M):A concentration unit defined to be

the number of moles of solute per liter of solution (mol/L).The concentration (molarity) of water is 55.5 mol/L or 55.5M.

The concentration of compound X is 5 mM (5 mmol/L).

Compound X is present in 5 millimolar concentrations.There are 5 millimole of compound X in 1 liter of solution.

There are (5103) (6.022 1023) molecules of compound X

in 1 L of solution.


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(5) Metabolome & Metabolomics

Metabolome:The entire collection of small molecules in a given cell.

100~200 small organic molecules (metabolites) in mM or M.

Primary Metabolites LowMrintermediates in the major

metabolic pathways occurring in nearly every cell types.

Secondary metabolitesSmall set of metabolites specific to certain

types of cells or organisms.

Plant secondary metabolites: flavonoids, alkaloids, etc.


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Metabolomics:The quantitative measurement of all low molecular

weight metabolites in an organism's cells at a specified time underspecific environmental conditions.

Provides a holistic view of the biochemical status or

biochemical phenotype of an organism.

Plant metabolomics for discovery of useful compounds,

food quality, etc.

Human metabolomics in health, diagnosis of disease, etc.

(see Addn reading.)

Blood cholesterol level Blood lipids profileBlood metabolomics


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(6) Macromolecules:HighMrpolymers assembled from relatively simple precursors.

amino acidsnucleotides

sugars (glucose, etc)


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(7) Oxidation and Reduction

Inorganic Chemistry:

Oxidationloss of electron(s), increase in oxidation number.

Reductiongain of electron(s), decrease in oxidation number.

Reduction(oxid # of oxygen, 0 to2)

4Fe2+(aq) + 4H+(aq) + O2(aq) --> 4Fe3+(aq) + 2H2O(l)

Oxidation(oxid # of Fe, +2 to +3)

Iron is oxidized by O2, which is an oxidizing agent.

In turn, O2is reduced.


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Organic Chemistry:

Oxidationof carbon atoms:

Reactions that remove H atoms from C atoms and/oradd O, N, or halogen atoms to C atoms.

Reductionof carbon atoms:

Reactions that add H atoms to C atoms and/or

remove O, N, or halogen atoms from C atoms.

Ox Ox

RCH2CH2R RCH=CHR RCCR

Red Red

RCH3 RCH

2OH RC(=O)H RCOOH

RCH2 RCH(OH)R RC( O)R

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