The Official DNA Structure Thread

[Sea of ASH]

i was going over it today and i was pretty amazed at the whole structure and the different bonds involved.

so i think/hope this is a good thread to start a DNA discusion


There are 3 parts to DNA

1)the deoxyribose sugar

• missing an OH in its carbon #2
• 5 carbon sugar that forms a 5 member ring in which O is included

2)the nitrogenous base

• binds to the sugar at its carbon #1 to form a beta-N-Glycosidic linkage
• Types of bases: A,T,G,C ----> PUR As Gold CUT the PYE
• pur's pair up with pye's (therefore 50/50 ratio of them)
• A-T contain 2 H-bonds and C-G contain 3 H-bonds
• van der Waals interations between the bases that above and below it
• called bases becuz they contain basic -NH2
• they are inside the helix structure of DNA

NOTE: SUGAR + BASE = NUCLEOSIDE
NOTE: SUGAR + BASE + 3 PHOSPHATE GROUPS = NUCLEOTIDE
NOTE: the sugar and phosphate make the backbone


3)the phosphate group

• attached to the sugar at its carbon #5 to form phosphodiester linkages
• during polymerization two phosphates break off and one is left to form the linkage
• are acidic, hence the name nucleic acids

NOTE: 5' END OF DNA IS THE FREE PHOSPHATE GROUP AND THE 3' IS THE FREE OH GROUP

the 5' end of one strand is connected to the 3' end of another, therefore they are said to run "antiparallel"

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[Sea of ASH]

btw please feel free to add, edit, comment or whatever else to this...

 

[userah]

I guess you can add that if there are more G-C bases, it increases the boiling point of the DNA (sort of a given if you understand that they have more H bonds thus increasing boiling point)

I forget if it's A-T or G-C ones that make the DNA more fluid. I think it's A-T but i could be wrong. hopefully someone clarifies.

 

[bigstix808]

I guess you can add that if there are more G-C bases, it increases the boiling point of the DNA (sort of a given if you understand that they have more H bonds thus increasing boiling point)

I forget if it's A-T or G-C ones that make the DNA more fluid. I think it's A-T but i could be wrong. hopefully someone clarifies.

you're right.

A-T (A-U) joins with 2 H-bonds, whereas C-G bonds with 3 H-bonds making it more "rigid"

 

[Sea of ASH]

ya thats right, G-C rich DNA's tend to have a higher BP due to the extra hydrogen bond.

question: why doesnt water H-bond with the bases?

 

[osimsDDS]

10 base pairs per turn or twist (34 angstroms)...and i think the width is 2 angstroms but i am not sure...haha you prob dont need to know that ahaha

 

[osimsDDS]

i was going over it today and i was pretty amazed at the whole structure and the different bonds involved.

so i think/hope this is a good thread to start a DNA discusion


There are 3 parts to DNA

1)the deoxyribose sugar

• missing an OH in its carbon #2
• 5 carbon sugar that forms a 5 member ring in which O is included

2)the nitrogenous base

• binds to the sugar at its carbon #1 to form a beta-N-Glycosidic linkage
• Types of bases: A,T,G,C ----> PUR As Gold CUT the PYE
• pur's pair up with pye's (therefore 50/50 ratio of them)
• A-T contain 2 H-bonds and C-G contain 3 H-bonds
• van der Waals interations between the bases that above and below it
• called bases becuz they contain basic -NH2
• they are inside the helix structure of DNA

NOTE: SUGAR + BASE = NUCLEOSIDE
NOTE: SUGAR + BASE + 3 PHOSPHATE GROUPS = NUCLEOTIDE
NOTE: the sugar and phosphate make the backbone


3)the phosphate group

• attached to the sugar at its carbon #5 to form phosphodiester linkages
• during polymerization two phosphates break off and one is left to form the linkage
• are acidic, hence the name nucleic acids

NOTE: 5' END OF DNA IS THE FREE PHOSPHATE GROUP AND THE 3' IS THE FREE OH GROUP

the 5' end of one strand is connected to the 3' end of another, therefore they are said to run "antiparallel"

one more thing....its not the 5' end of the DNA its the 5' CARBON of the sugar deoxyribose that has the PHOSPHATE GROUP and the 3' CARBON has the OH group....The 5' carbons with the phosphate group attached to the next 3' carbon with OH group via a phosphodiester bond...this bond has a high angle strain and therefore the DNA twists on itself...

 

[Sea of ASH]

10 base pairs per turn or twist (34 angstroms)...and i think the width is 2 angstroms but i am not sure...haha you prob dont need to know that ahaha

the width is actually 20 A apart...
1A = 10^-10 m

 

[osimsDDS]

yea good call i knew it started with a 2 tho..haha

 

[Sea of ASH]

one more thing....its not the 5' end of the DNA its the 5' CARBON of the sugar deoxyribose that has the PHOSPHATE GROUP and the 3' CARBON has the OH group....The 5' carbons with the phosphate group attached to the next 3' carbon with OH group via a phosphodiester bond...this bond has a high angle strain and therefore the DNA twists on itself...

exactly thats y they call it the 5' end.... kinda like for proteins how its the N and C terminus. the naming is based on the linkage to the carbons on the sugar.

 

[AndyK]

Adenine, Guanine = Purines (two rings... I know of only one mnemonic for this: aggies are pure )

Thymine, Cytosine, Uracil = Pyrimidines (one ring)

Adenine <-two H-bonds-> Thymine
Cytosine <-tree H-bonds-> Guanine

That's why many proteins involved in transcription associate with AT-rich regions... because they are more easily separated from eachother.

Adenine is found in many other biochemical forms such as ATP, ADP, cAMP, FAD/H, NAD/H and others. Guanine is present in GTP and GDP. Note that both are purines.

Note that the DNA double helix has areas where the sugar-phosphate backbones are closer together and areas where they are further apart. These are known as minor grooves and major grooves, respectively. If the two backbones are further apart, that means the bases are more "visible" to transcription factors, therefore this is where they commonly bind.

 

[theedaddy77]

NOTE: SUGAR + BASE = NUCLEOSIDE
NOTE: SUGAR + BASE + 3 PHOSPHATE GROUPS = NUCLEOTIDE

so yeah nucleotide have what type of bond that connects them a dn nucleoside has what type of bond that connects them?