DNA

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

Topoisomerase is responsible for eliminating supercoiling in DNA. The tension holding the helix in its coiled and supercoiled structure can be broken by nicking a single strand of DNA. Try this with string. Twist two strings together, holding both the top and the bottom. If you cut only one of the two strings, the tension of the twisting is released and the strings untwist.
Helicase accomplishes unwinding of the original double strand, once supercoiling has been eliminated by the topoisomerase. The two strands very much want to bind together because of their hydrogen bonding affinity for each other, so the helicase activity requires energy (in the form of ATP ) to break the strands apart. While some DNA polymerases can unwind DNA during their synthesis of new DNA, helicase increases efficiency in the process and impeding helicase activity would slow replication .
DNA polymerase proceeds along a single-stranded molecule of DNA, recruiting free dNTP's (deoxy-nucleotide-triphosphates) to hydrogen bond with their appropriate complementary dNTP on the single strand (A with T and G with C), and to form a covalent phosphodiester bond with the previous nucleotide of the same strand. The energy stored in the triphosphate is used to covalently bind each new nucleotide to the growing second strand. There are different forms of DNA polymerase , but it is DNA polymerase III that is responsible for the processive synthesis of new DNA strands. DNA polymerase cannot start synthesizing de novo on a bare single strand. It needs a primer with a 3'OH group onto which it can attach a dNTP. DNA polymerase is actually an aggregate of several different protein subunits, so it is often called a holoenzyme. The holoenzyme also has proofreading activities, so that it can make sure that it inserted the right base, and nuclease (excision of nucleotides) activities so that it can cut away any mistakes it might have made.
Primase is actually part of an aggregate of proteins called the primeosome. This enzyme attaches a small RNA primer to the single-stranded DNA to act as a substitute 3'OH for DNA polymerase to begin synthesizing from. This RNA primer is eventually removed by RNase H and the gap is filled in by DNA polymerase I.
Ligase can catalyze the formation of a phosphodiester bond given an unattached but adjacent 3'OH and 5'phosphate. This can fill in the unattached gap left when the RNA primer is removed and filled in. The DNA polymerase can organize the bond on the 5' end of the primer, but ligase is needed to make the bond on the 3' end.
Single-stranded binding proteins are important to maintain the stability of the replication fork. Single-stranded DNA is very labile, or unstable, so these proteins bind to it while it remains single stranded and keep it from being degraded.

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'.