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Backbone is comprised of?
- 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
____________keeps neucleiotides bonded covalently
In what direction does the DNA and RNA synthesis proceed in
5' to 3' direction
Where is information found in DNA
- Base pairs
- Stacked on top of one another forming parallel planes
What is the orientation of the polynucleotide strands in the double helix?
Bases are stabilized with?
Primarily with Hydrogen bonds
Most DNA in cells is right or left handed helix?
Right handed helix
B form of DNA
- -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.
B DNA can_____ about it's long axis. Which is important why?
- It can bend along its long axis
- It is important in DNA- protein interactions and in the folding of DNA into compact condensed structures
DNA denaturation andrenaturation is important when?
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.
Can RNA fold
- Yes, it has many secondary structures
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
- R groups points outwards
stabolilized by H bonds
Why is Proline compact?
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
- 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)
Motif and Domain
- 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
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