Business

• Buy your lab manual ASAP,

– Today, Monday, 3 - 4 PM, BI412, JY’s office, ($3.00 cash),– Read the assigned lab modules,

• Molecular Models,

• Techniques and Calculations,

– 201 Lab web site…go to courses from the Biology Home Page,

• Quiz Thursday covering reading materials through that day, i.e. Proteins.

Buffers

…a solution characterized by the ability to resist changes in pH when limited amounts of acid or base are added to it,

Buffers Minimize pH Changes

bufferedsolution.

unbufferedsolution.

Organic Molecules

…compounds synthesized by living systems, usually carbon compounds,

…once thought to derive from living systems only, now known to (also) originate from inorganic systems.

Inorganic Compounds

…molecules derived from processes not associated with living systems.

Vitalism

…the belief that complex molecules found in living organisms could only be synthesized by a ‘life force’ outside the jurisdiction of physical and chemical laws.

Urea

1828: when trying to synthesize the inorganic salt ammonium cyanate, Friedrich Wöhler accidentally made urea, an ingredient of urine,

– to the Vitalists…‘I must tell you that I can prepare urea without requiring a kidney or an animal, either man or dog’.

Wöhler Rebuked

…however, the cyanic acid had been obtained from animal blood,

…the Vitalists claimed that Wöhler’s mistake ‘proved’ Vitalism.

Wöhler’s Student Kolbe

…Hermann Kolbe soon thereafter synthesized acetic acid from ‘pure’ elements, vindicating Wöhler,

…today we can synthesis just about any organic molecule.

Modern Organic Chemistry

…in the 20th century, we can synthesize all types of organic molecules de novo, including,

– DNA

– RNA

– Protein

– Lipid

– Carbohydrate,

Moreover, we can harness biological systems to synthesize unique organic molecules using the techniques of biotechnology.

Mechanism

…mechanist theory: that all natural phenomena, including the processes of life, are governed by physical and chemical laws,

…replaced the Vitalist theory.

Major Elements of Life

Carbon

Hydrogen

Oxygen

Nitrogen

Sulfur

Phosphorous

CHONSP

Carbon

…cells are composed of 70% to 95% H2O,

– proteins, nucleic acids, carbohydrates, lipids and other molecules differentiate living systems from inanimate materials,

...carbon atoms form the backbone for most of these molecules.

Carbon is Tetravalent

…carbon has six electrons, two in its inner shell, and four in its outer shell,

– thus not likely to form a covalent bond with a single molecule,

…usually forms four covalent bonds.

Valence

…valence is the number of covalent bonds an atom will usually form,

…equal to the number of electrons required to fill the outer shell.

CO2

…four covalent bonds for carbon, two each for oxygen.

O C O

Urea Again

C (4), O (2), N (3), H (1)

Carbons Form the Backbone of Many Organic Molecules

Hydrocarbons

…hydrocarbons: molecules containing only carbon and hydrogen.

Fig. 4.4

Carbon Skeletons

…form the backbones of many organic molecules and contribute to their diversity.

Carbon’s Versatility

In Vino, Veritas

Isomer

…one of several organic compounds with the same molecular formula, but with different structures and therefore properties,

Structural Isomers

Geometric Isomers

Optical Isomers

Structural Isomers

Geometric Isomers

Enantiomers = Optical Isomers

functionalgroups.

Enantiomers = Optical Isomers

functionalgroups.

Functional Groups

...the components of organic molecules that are most commonly involved in chemical reactions,

-OH

-CHO

-COOH

-NH2

-OPO32-

-SH

Functional Groups determine chemical reactivity.

The Whole is the Sum of the Parts

…functional groups behave consistently from molecule to molecule,

…it is the number and arrangement of the functional groups in concert with the carbon backbone that determines each molecule’s unique properties.

Ducks!

Reactivity is stereo specific.

Hydroxyl Group

…a hydrogen atom is bonded to an oxygen atom which in turn is bonded to the carbon skeleton,

Alcohol

…small alcohol molecules are soluble because of hydrogen bonding,

-

+

...larger alcohol molecules are usually not soluble.

Solubility is Important

…hydroxyl groups are present in sugars and are responsible for their solubility,

Carbonyl Group

…consists of an oxygen atom double bonded to a carbon atom.

Carbonyl Group (Aldehyde)

…consists of an oxygen atom double bonded to a carbon atom at the end of a molecule,

Carbonyl Group (Ketone)

…consists of an oxygen atom double bonded to a carbon atom in the middle of a molecule,

Got it?

Aldehyde

Ketone

altitude?

Carboxyl Group

…a carbon atom double bonded to an oxygen atom and to a hydroxyl group,

Carboxylic Acids

…carboxyl groups act as acids,

donates H+

Formic and Acetic Acid(examples)

…formic acid (HCOOH): stinging part of an ant bite,

…acetic acid:

…vinegar, Lemon Heads, etc.

Amino Group

…a functional group that consists of a nitrogen atom bonded to two hydrogen atoms,

Amino Groups Act as Bases

• This give the amino group a charge of +1, its most common state within a cell.

Amino Acids

…an organic molecule possessing both carboxyl and amino groups,

…amino acids are the monomers in polypeptides (proteins).

3+ -

Phosphate Group

…phosphate is an anion that is formed by dissociation of an inorganic acid H3PO4,

DNA

Phosphate Groups as Backbones

Phosphate Groups as Lightning

ATP: adenosine triphosphate.

ATPases, Molecular Pumps

ATP ADP+ P

H+

H+

cell membrane

Sulfhydryl Group

…hydrogen atom is bonded to a sulfur atom which in turn is bonded to the carbon skeleton,

Disulfide Bonds

Look Here.

To Do

• Read through pp. 58-60, and pp. 65-68,

• Prepare for lab Thursday,

• Prepare for Quiz Thursday.