DNA Structure & Replication Flashcards
Conservative model of DNA replication
Parental DNA strand creates a separate identical daughter strand. There is no sharing between the two.
Semiconservative DNA replication
The parental DNA splits in half and creates two daughter DNAs that share one half a new strand, one half old strand.
Dispersive DNA replication
The parental DNA splits into two collection of pieces which are filled with new DNA pieces. All daughter strands contain bits and pieces of the parental strand.
Meselson-Stahl “The Most Beautiful Experiment”
In 1958, Matthew Meselson and Frank Stahl figured out which of the three models of DNA replication was correct using heavy N15 labeled DNA and N14 amino acids. They then put the DNA in a centrifuge with test tubes to see what pattern would arise.
Nucleophile attack
When a strongly electronegative atom such as oxygen attacks, a less electronegative atom
Hydrolysis reaction
When a nucleophile is part of a water molecule
Gamma phosphoryl
What is attacked in ATP hydrolysis and results in ADP + P1
Nucleophilic substitution
The three prime oxygen in a DNA backbone attacks the alpha phosphoryl group of the incoming dNTP
DNA polymerase III
Holds base pairs in place and creates the correct chemical environment so that synthesis reaction can occur. The hand thing.
DNA polymerase palm
The active site and the proofreading site
DNA polymerase fingers
Grip incoming dNTP and create a 90° bend in template DNA
DNA polymerase thumb
Interacts with newly synthesized DNA to stabilize the primer and maintains contact with the primer. It also stabilizes DNA and increases processivity.
Processivity
The rate at which we can add nucleotides, the rate of replication
Kinetic pause
Allows for time to move from active site to proofreading site
Replication fork
The active area of DNA were replication takes place
Leading strand
The piece of DNA that is being replicated in a continuous manner
Lagging strand
The piece of DNA that is being replicated in a discontinuous manner
Okazaki fragment
The peace of DNA that is replicated onto the lagging strand
Topoisomerase
The protein that is used to untwist helical DNA, it relieves overwhelmed DNA making sure it is ready to be opened up. It does this by making a small cut in one of the two DNA strands then resealing it
Helicase
The protein that opens up DNA for replication. It uses ATP to break the hydrogen bonds between DNA.
Beta sliding clamp
The protein attached to polymerase III that increases processivity and allows replication to speed up in a controlled way
DNA polymerase I
The polymerase that removes RNA primers in the processing of DNA after replication
SSB or single-stranded binding protein
Protects the part of the lagging strand that’s not being replicated yet. Keeps DNA from attaching to itself
Clamp loader
Uses ATP to attach the beta clamp to DNA to help increase processivity
DNA primase
Places in RNA primer so that DNA has a 3’ location to build from
RNA primer
Provides a 3’ location so that DNA replication can happen as DNA must be built 3’ to 5’
DNA ligase
Seals the nick in the DNA backbone left behind after polymerase I replaces RNA primers with DNA
DNA and RNA composition
Phosphate, pentos sugar, nitrogenous base
Nucleoside
Just the base and a sugar
Nucleotide
The base, sugar and five prime phosphate in a DNA structure
Pyrimidine
Uracell, cytosine, and thymine
Purine
Adenine, and guanine
DNA consists of
A pento sugar, a phosphate, and a nitrogenous base
What are the four DNA nucleotides?
Deoxyadenosine, deoxyguanosine, deoxythymidine, deoxycytidine
Phosphodiester bond
The phosphate that is bonded between two pinto sugars in the DNA backbone
Chromosome
Higher order structures of DNA and protein
Chromatin
A region of DNA and its associated proteins
DNAase I
A nuclease that digests unprotected DNA
Heterochromatin
Highly condensed, gene poor, transcriptionally inactive sections of DNA
Euchromatin
Less condensed, Gene rich, transcriptionally active sections of DNA
Chromatin remodeling complexes or CRCs
ATP dependent, multi-protein complexes that catalyze nucleosome sliding, exchange, and transfer. Allow us to change the histone core. Their primary use is to alter structure.
