DNA

hereditary traits result from info encoded in genes being deciphered into proteins
The information in genes codes for what?  
chromatin complex of eukaryotic chromosomes composed of 60% protein and 40% DNA
What is chromatin?  
nucleotides DNA & RNA building blocks
What are the building blocks for DNA and RNA?  
DNA two antiparallel strands of nucleotide chains held together by hydrogen bonds between the nitrogen bases

Consider:  If the DNA double helix is similar to a twisted ladder, the alternating units of phosphate groups and sugars makes up the sides holding the rungs together.
Describe DNA.  What type of bond holds the two strands of nucleotide chains together?  
nucleic acids made up of organic nitrogen bases, sugar, phosphate
What makes up nucleic acids?  
nitrogenous bases cytosine, thymine (DNA) or uracil (RNA): single ring pyrimidines

guanine, adenine:  double ring purines

What distinguishes one nucleotide from another?

Which nitrogenous base is used by RNA?

 
phosphodiester bond chemical bond connecting one nucleotide with the next one along the nucleic acid chain (phosphate group of one with hydroxyl group of another)
What bond holds one nucleotide with the next within the nucleic acid chain?  
hydrogen bonds hold together two antiparallel strands of nucleotide chains (DNA) by stabilizing complimentary nitrogen bases; adenine-thymine pairs have 2 hydrogen bonds between them and guanine-cytosine pairs have 3 between them
 What is the role of the hydrogen bonds in DNA structure?  How many hydrogen bonds are between the A-T pair and how many between the G-C pair?  
phosphate release supplies energy for making DNA molecule
endergonic synthesis of DNA
What supplies energy for the endergonic process of DNA synthesis?  
semiconservative method each original strand is used as template to build new strand in DNA replication
By what method does DNA replicate?  
DNA polymerase III

 

 

DNA polymerase I

enzyme that catalyzes the synthesis of new DNA molecule (bacteria) ...DNA polymerase can add free nucleotides to only the 3' end of the newly-forming strand. This results in elongation of the new strand in a 5'-3' direction.

 

erases primer and fills gaps

What catalyzes the synthesis of a new DNA molecule?

What enzyme is required to remove and replace the primer segments?

 
DNA primase creates a short RNA primer (required by DNA polymerase III) complementary to the DNA template
What is the role of DNA primase? Consider:  RNA that is complementary to a DNA template would consist of the following:  DNA is T then RNA is A; DNA is A then RNA is U; DNA is G then RNA is C; DNA is C then RNA is G.
DNA helicase  use hydrolysis of ATP to increase efficiency of unwinding the double helix of DNA in front of polymerase
What enzyme unwinds the double helix?  
initiation the step in DNA replication in which the replication proteins open up the double helix and prepare for complementary base pairing
Describe initiation  
DNA gyrase relieves torque (torsion strain on the two strands)
What relieves the torsion strain during DNA replication?  
DNA ligase continuously required during DNA replication to join together fragments of lagging strand; DNA repair
What is the role of DNA ligase? Consider:  The leading strand is synthesized by DNA pol III as a continuous strand...the lagging strands are synthesized in Okazaki fragments.
 elongation  the step in DNA replication in which the proteins connect the correct sequence of nucleotides into a continuous new strand
 Describe elongation.  
Chargaff's rules A pairs with T and G pairs with C; so %A = %T, %G = %C and %A + %T + %G + %C = 100
Chargaff's rules pairs what complementary nitrogenous bases together allowing an equal distribution of weight in the double helix? Consider:  If you know that the DNA nucleotides is made up of 30% Thymine, how much of each other nitrogenous base is there? (just an example problem to get you to think about it)
pyrophosphate by-product of DNA synthesis
RNA primer required for DNA polymerase to begin DNA replication
discontinuous synthesis lagging strand's replication with segments of Okazaki fragments
Okazaki fragments are involved in what kind of synthesis on which strand?
Consider:  The lagging strand is replicated with stretches of Okazaki fragments and that is why its synthesis is considered to be discontinuous.
3' end new bases are always added to it during replication
5' to 3' direction new DNA strand (leading) is synthesized in this way
Reading of bases starts on which end?  New bases are added to which end?  The new DNA strand is synthesized in what direction?  
alternating sugars and phosphates side supports of double-stranded DNA
DNA replication two strands separated; each strand is used as a template for making a new duplex; synthesis on each strand is in the opposite direction; each nucleus contains one strand of the original DNA and one strand of the newly synthesized DNA
What are the basic steps in DNA replication?  
5 number of nitrogen bases for use in DNA and RNA
be able to identify complement to DNA sequence  
DNA coding for proteins sequence of amino acids, which make up proteins, was determined by the nucleotides in a gene sequence
primosome primase, helicase, & accessory proteins
replisome large macromolecular assembly consisting of primosome & complex of 2 DNA pol III enzymes
The replisome consists of what?  
replication fork site of the opening of the DNA strands where active replication occurs
What is the replication fork?  
time constraints on eukaryotic DNA replication avoided by multiple origins of the replication from each chromosome, which results in multiple replicons
How is time optimized during eukaryotic DNA replication?  
 termination  the step in DNA replication in which two replication forks moving in opposite directions may meet
 When does termination occur?  
DNA polymerase I erases primer & fills gap; makes first repair of mistakes made during DNA replication
What is the role of DNA polymerase I?  
synthesis of lagging strand Primase adds RNA primer ahead of 5' end, DNA polymerase III adds nucleotides to primer until gap is filled in, DNA polymerase I replaces primer with DNA nucleotides, and ligase seals the gap.
What are the steps in synthesis of the lagging strand?  
Watson & Crick proposed double helix model of DNA
Who proposed the double helix model of DNA?  

The Enzymes of DNA Replication

Essay

1.  Describe the steps in the replication of a double stranded DNA molecule as discussed in lecture. Include the following terms: DNA polymerase, replication forks, helicase, leading and lagging strands, Okazaki fragments, primase, ligase, semiconservative replication, topoisomerase, 3' to 5', 5' to 3'.