-
Backbone is comprised of?
- repeating phosphate pentose units.
- Sugar phosphate backbone
- Oriented to the outside of the double helix
- Doesnt contain information
-
5' end
free phosphate group on the 5' carbon of the terminal sugar
-
3' end
free hydroxyl on the 3' carbon of the terminal sugar
-
____________keeps neucleiotides bonded covalently
Phosphodiester bond
-
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?
Antiparallel
-
-
-
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
-
A DNA
- 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
-
Z DNA
- 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.
-
Tm ??
- 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
- hairpin
- stem-loop
- psedoknot
-
Proteins?
Function is derived from the 3 dimentional structure, and the 3 dimentional structure is specified by the amino acid sequence.
Three dimentional structure= conformation
-
Primary structure?
- 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
-
Secondary Structure
- 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
-
Alpha helix
- H bonds (stabilizes)
- R- group point outwards
-
Beta sheets
- Laterally packed strands
- H-bonding between backbone of the beta strands
- not very long
- parallel or antiparallel
- pleated
- R groups points outwards
-
Beta Turns
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
-
Tertiary structures
- 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
-
Quaternary structure
- Some protein need association with other polypeptides
- Example:
- Potassium Ion Channel; nearly identical polypeptides that create the channel. It takes 4!
-
Supramolecular Structure
- 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
|
|