“molecular workbenches” protein structure

“Molecular Workbenches”Protein structure

Life is a system of elements that can replicate the entire set of elements from rudimentary parts to form new copies of the whole system.

Elements: Are large, macro-molecules, such as DNA, RNA and proteins, with 1000’s of covalently linked atoms.Rudimentary Parts: Are the building blocks for the elements. DNA and RNA are made from nucleic acids; proteins are made from amino acids. These are small molecules held together by covalent bonds.

Two Types of AtomicInteraction:

Covalent Bonds(make molecules)

Non-covalent Bonds(make molecules come alive)

Two Types of CovalentBond:

Non-polar(electronically balanced)

Polar(electronically unbalanced)

Molecules “see” eachother by non-covalentinteractions of their

electron shells.

4 Types ofNon-covalent Bonds: (1) van der Waals(2) hydrogen bonds(3) ionic(4) hydrophobic effect

Covalent and non-covalentChemical bonds:

Bond type length (nm) strength (kcal/mole)in vacuum in water

Covalent 0.15 90 90Non-covalent: ionic 0.25 80 3

hydrogen 0.30 4 1van der Waals 0.35 0.1 0.1

Living things have very high

information content.

Proteins are amino acid polymers.

Amino Acids

Building Molecules:The Condensation

Reaction

Four levels of proteinStructure:

1°-aa sequence2°-local folds/structure3°-structure of polypeptide4°-polypeptide interactions

Two common folds:-helix-sheet

cytochrome b

NAD-binding

antibody

Next Class-Protein Function:

How we studyproteins