BIOL 200

• repeating phosphate pentose units. 
• Sugar phosphate backbone
• Oriented to the outside of the double helix 
• Doesnt contain information 

free phosphate group on the 5' carbon of the terminal sugar

free hydroxyl on the 3' carbon of the terminal sugar

Phosphodiester bond

5' to 3' direction

• Base pairs
• Stacked on top of one another forming parallel planes

Antiparallel

• Thymine 
• 2 hydrogen bonds

• Guanine 
• 3hydrogen bonds 

Primarily with Hydrogen bonds

Right handed helix

• -In B form the majority of time 
• -2 helical grooves (Major and minor grooves)
• -This is important  because it is where protein interacts with the nucleic acid. Basically protein acess to basse pairs

• In very low humidity (and dehydrated samples), the B form of DNA changes to the A form. Also RNA-DNA and RNA-RNA helices exist in the A form.
• Found in in vitro 

• Short DNA molecules of alternating purine and pyrimidine nucleotides
• Adopt a left-handed helix conformation known as the Z form
• Z DNA is also transiently formed shortly after transcription and, as such, is a tag for actively transcribed genes.

• It can bend along its long axis
• It is important in DNA- protein interactions and in the folding of DNA into compact condensed structures 

During DNA replication and intranscription. It is also exploited in many techniquesin molecular biology and genomics.

• It is a function of GC conent because it takes more energy because of the 3hydrogen bonds 
• As we increase the percentage of CG bonds the higher the Tm temperature. 

• Yes, it has many secondary structures 
• hairpin
• stem-loop 
• psedoknot

Function is derived from the 3 dimentional structure, and the 3 dimentional structure is specified by the amino acid sequence.

Three dimentional structure= conformation 

• They have a bias
• 
• What binds amino acids together is the peptide bond
• 

• Linear arrangement
• Also use the term residue=amino acid within the peptide/polypeptide

• Refers to interactions at a local level 
• Folding of localized regions of a polypeptide chain 
• Stabilizing non-covalent interactions, forming as example:
• Alpha helices
• Beta sheets
• Beta turns

Non covalent interactions=random coil 

• H bonds (stabilizes)
• R- group point outwards

• Laterally packed strands 
• H-bonding between backbone of the beta strands 
• not very long
• parallel or antiparallel
• pleated 
• R groups points outwards

stabolilized by H bonds

Because ring structures forces a natural bend. In other words the bends are rich in glycine and proline 

• Long range of folding with a polypeptide chain 
• Stabilized by:
• hydrophobic interactions between non polar side chains
• hydrogen bonds between polar side chains 
• disulfide bond between cysterine residues
• Provides a compact structure of alpha helices, beta sheets and turns

• Some protein need association with other polypeptides
• Example:
• Potassium Ion Channel; nearly identical polypeptides that create the channel. It takes 4!

• Macromolecular assemblies
• Usually>1 megadaltons in size 10's to 100's of polypeptides chains(as well as other macromolecules)

• 3 different motifs
• a) coiled- hydrophobic residue 
•              - found in very fibrous proteins 
• b) Ef Hand/ helix loop-helix motif
•               - ionic bonds involving a Ca²⁺ 
•              -Ca2+ binding protein 
• c) Zinc finger motif
•              -allows polypeptides to interact with DNA          and RNA 
•              - RNA and DNA binding proteins

• Many polypeptides are composites of different combinations of motif/ domains
• * concerve domain,interchange of domain....which create new protein