April 7th - Monday

Corrections: (4/13/08) Apologies for those who couldn't find this entry! I mislabeled the date April 4th - whoops!

It has been (obviously) corrected. Thanks to those that spotted the error!

Chapter 16 -- Molecular Genetics:

~Thanks for being patient with me as I go back and clean-up these messy notes!

During the middle stuff, we looked at complementing slides, so if you're lost, its most likely because I wrote some explanatory notes to myself.

Edited ~(9/4/08)

DNA STRUCTURE:
1.) Double Helix
2.) Sugar (deoxyribose) -- Phosphate -- and Nitrogenous Base (nucleotide)
3.) Nitrogenous Bases are the Purines--(Adenine, Guanine) and the Pyrimidines (Thymine, Cytosine)
4.) It has a sugar-phosphate backbone with nitrogen groups towards the middle.
5.) the two DNA strands are complementary. (A = T) (G =- C) Note: (Adenine + Guanine) have two lines between them because there are two hydrogen bonds holding them together. In the second example, we have three lines between (Guanine + Cytosine), representing its three hydrogen bonds.
6.) Polarity: The 5' end is always the Phosphate ( P) The 3' end is always the Hydroxide (OH) Antiparallel:where one pair is 5' to 3' and the other is 3' to 5' - opposite ends. 5' (P) --------------------------- (OH) 3' 3' (OH) --------------------------- (P) 5'
General Stuff: DNA length is measured in "base pairs" - abbreviated to "bp" ( i.e. -- how many pairs of A&T and C&G you've got) One thousand base pairs (1000 bp) is called a Kilobase (1 kb).

DNA Replication:

Semi-Conservative Replication: one parental strand acts as the template (old strand) for the synthesis of the new complementary strand.

(So 1 old strand + one new strand = a new DNA double helix)

DNA Replication is Fast: ~50-500 nt (nucleotides)/sec.
In humans, it takes a few hours to replicate and we have 6 x 10⁹ bp (six billion)
It's also accurate ~1 mistake per billion (10⁹) nucleotides

Mechanism of DNA replication:

1.) Origins of Replication - origins are particular cites on DNA ( "ori" sites - it's pronounced like the cookie - "Oreo's")

Only 1 ori per chromosome in bacteria.
Eukaryotes: 100 to 1000 ori's per chromosome - replication is faster (more Ori's)

get bigger & eventually contact with one another, and finally get two daughter DNA molecules

2.) DNA is synthesized in the 5' to 3' direction only. (fig 16.13)

(the lowercase 'd' in the names is for deoxyribose)

When a nucleotide is added to DNA, pyrophosphate (P-P) is released (two phosphates linked together).

Then, that (P-P) is broken down into 2Pi (two inorganic phosphates) - which releases energy to drive synthesis.

Enzymes for DNA Replication
1.) Helicase- unwinds the DNA at the replication fork & separates the two strands.
2.) Single strand binding protein (SSBP) - binds to single strand of DNA, protects DNA from being recognized as "damaged" DNA till time for replication (NOT AN ENZYME!) - Don't say I didn't warn you.
3.) DNA polymerase - synthesizes DNA. can only add nucleotides to an existing strand of DNA or RNA cannot start DNA synthesis by itself. it needs a primer- (a piece of DNA or RNA)
4.) RNA primase: makes a short (~10 nucleotides (nt) long ) fragment of RNA that serves as a starting point for elongation by DNA polymerase.
5.) DNA ligase = ("ligate"- meaning to join) Joins together Okazaki fragments on the lagging strand.

So, using the above ingredients, let's look at the steps for making this new DNA....

Process of DNA Synthesis:
1.) Helicase undwinds the DNA.
2.) Single strand binding proteins bind the single strand DNA to stabilize it.
3.)Primase synthesizes a primer for the leading strand at the origin. Synthethize many primers for the lagging strand - each Okazaki strand has (& needs) an RNA primer.
4.) DNA Polymerase elongates the leading strand & elongates the short Okazaki fragments. it can (and must) remove the RNA primer & replace them with DNA so the strand has no remaining RNA in it.
5.) DNA ligase- joins okazaki fragments together into 1 long strand

Last edited on 04/14/2008 08:40 by girlgenius

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