6/21/01

Lecture #1 - Protein and DNA Structure

Proteins (or polypeptides) are formed from amino acids.

Two amino acids may combine in a condensation reaction (a molecule of water is lost) to form a dipeptide (polypeptide). The peptide bond (bond between carbonyl carbon and amide nitrogen) has partial double bond character due to resonance from the carbonyl group. for this reason rotation about the C-N bond is limited.

The peptide bond structure also gives polypeptides a polarity. the amino (N) terminus is conventionally written at the left and the carboxyl (C) to the right.

The structure of amino acids and polypeptides is important to know.

The R group creates the diversity in proteins. 20 different R groups are found in most organisms.

R groups can be classified into several types.

neutral and hydrophobic: alanine, valine, leucine, isoleucine, proline, tryptophan, phenylalanine, methionine.
neutral and polar: glycine, serine, threonine, tyrosine, cysteine, glutamine, asparagine.
basic (this refers to their ability to be protonated, not to pH): lysine, arginine, histidine.
acidic( this refers the their ability to lose a proton, not to pH): aspartic acid, glutamic acid.

Alternative R group classification:

aromatic amino acids: tryptophan, tyrosine, phenylalanine.
sulfur-containing amino acids: methionine, cysteine.
cyclic amino acids: proline.

One letter and three letter abbreviations for the 20 amino acids are important to know.

Protein Structure

primary structure - refers to the linear sequence of amino acids.
secondary structure - how the polypeptide folds into local strucutres (a-helix or ß-sheet)
tertiary structure - how the peptide backbone, R groups, and secondary sturctural features are arranged in space.
quaternary strucutre - association of polypeptides; can be dimers or multimers; can be homo or hetero multimers. (comprised of the same or different polypeptide units).

Forces that hold proteins together

covalent - the most common covalent bond is the disulfide bond. - occurs between proteins with cysteine residues - disulfide bonds can form intra-chain to aid secondary structure, or inter-chain to to form quaternary structure. insulin is an example of a dimer held together by disulfide bonds.
non-covalent - these are more important even though covalent bonds are energetically much stronger. many many non-covalent bonds sum over the entire macromolecule to create a large force.
- ionic bond - basic amino acid (K, R, H) with acidic amino acid (D,E). This is also known as a salt bridge.
- hydrogen bonds - an hydroxyl with a carbonyl or an amide with a carbonyl
- hydrophobic interactions - hydrophobic R groups associate with the goal of excluding water.
- van der Waals forces - very weak.

a -Helix

are held together by H-bonding between NH and C=O bonds on the backbone (not on the R groups).
each C=O is bonded to the NH four (a-carbons) down the polypeptide chain.
the R groups stick out from the center of the helix.
there are 3.5 amino acids per turn of the helix, and therefore 7 amino acids per two turns.
- R groups 1,4 and 7 are on one face of the helix
- R groups 2, 3, 5, and 6 are on the other face.
proline is a helix-breaking amino acid. its cyclic structure restricts bending at C-N bonds - polypeptide regions containing proline will not form a helix.
an example of a -helical protein is the a-keratin (major component of hair and fingernails).

Specialized a-Helices

amphipathic helix - a-helix with one face completely hydrophobic (non-polar) and one face completely hydrophilic (polar)
- these amphipathic a- helices are often form protein-protein interaction domains - hydrophobic faces of two a- helicies make contact and hold the dimers together via a hydrophobic interaction
"leucine zipper" helix - an amphipathic a-helix where every seventh amino acid (on the hydrophobic face) is leucine.
- leucine zippers are the dimerization interface in some important eukaryotic transcription factors.

ß-sheet

like the a-helix, the ß-sheet is held together by H bonds between the NH and C=O of the backbone, but the interactions are not local - rather they are between widely separated polypeptide segments of the same chain or between 2 polypeptides
small R groups like glycine and alanine are favored
it is called a "pleated" sheet because it rises and falles periodically.
B-sheets can be parallel: N --> C, N --> C or antiparallel: N --> C, C --> N
silk fibroin consists entirely of ß-pleated sheets.
most proteins are composed of both a-helix and ß-sheet configurations.

DNA Structure

There are two types of bases:

pyrimidines are 6-membered rings with two nitrogens. The N1 position is bonded to the sugar in DNA and RNA
purines have a 6-membered ring and a 5-membered ring with four nitrogens. the N9 position is bonded to the sugar in DNA and RNA.

The structures of the bases is important.

base + sugar = nucleoside

base + sugar + phosphate = nucleotide

sugars connect to the bases at the C-1' position on the sugar.

the sugar difference between DNA and RNA (no 2'-OH in deoxyribose) allows DNA to form B-form DNA - the presence of the 2' -OH group in RNA prevents RNA from adopting a B-form structure.

mono-, di-, and tri-phosphate nucleotides exist: AMP, ADP, ATP.

phosphates are labeled a, b, c. the a -phospate gets incorporated into the phosphodiester bond and therefore into the backbone of DNA/RNA.

DNA synthesis is directional, with new nucleotides being added to the 3' end by a phosphodiester bond.

B-form DNA

base pairing occurs in the center of the double helix.

C H-bonds with G and A H-bonds with T. A purine always bonds with a pyrimidine.

The two strands of DNA are antiparallel and complementary.

Forces which stabilize the DNA include:

hydrophobic interactions - bases are hydrophobicand are located in the in the center of the molecule away from the aqueous environment.
base stacking energy - planar aromatic rings on top of each other produce a van der Waals interaction.
phosphate backbones are negatively charged - the twists distribute this repulsive charge.
sugar-phosphate backbones - consist of many polar atoms - allow H-bonding with water on the outside.
specific H-bonding - A/T has 2 H bonds and C/G has 3 H bonds.

There are slightly more than 10 base pairs per turn of DNA.

DNA has a major groove and a minor groove.

Most protein-DNA interactions occur in the major groove - they have better access to the base sequence. This is particularly important for sequence-specific DNA binding proteins

B-form DNA is a right-handed helix.

Alternative nucleic acid structures.

A-form nucleic acids
occurs under low humidity, has 11 base pairs per turn, is right handed like B-form DNA and is shorter and fatter than B-form DNA.

double stranded RNA can take the A-form because it allows the presence of 2'hydroxyl groups on the sugar. B-form does not permit this, so RNA will never take that form. Hybrids of DNA and RNA will also take the A-form.

Z-form nucleic acids can be formed in a test tube only, is a lefthanded helix, requires special sequences of alternating purines and pyramidines. its importance in cells (if it has one at all) has not been definitively determined.