1. What is the role of nucleic acid?
2. What is the monomer of a nucleic acid?
3. The monomer of a nucleic acid is made up of 3 things: a phosphate, base, and a _________________.
4. What is the difference between DNA and RNA?
5. A always pairs with T, and G always pairs with ____.

Nucleotides
• Include DNA and RNA

Components of a Nucleotide
• Phosphate Group (5’ end)
• Pentose Sugar (3’ end)
• Ribose in RNA
• Deoxyribose in DNA
• Nitrogenous bases
• Purine (2 rings)
• Adenine, A
• Guanine, G
• Pyrimidines (1 ring)
• Cytosine, C
• Thymine, T (only in DNA)
• Uracil, U (only in RNA)

Formation of Polynucleotides
• Dehydration reactions link nucleotides together
• Phosphodiester linkages are the bonds between the sugar of one nucleotide and the phosphate of the next
• New nucleotides can only be added to the 3’ end where there is an exposed hydroxyl group (from the sugar)
• This is why we say that DNA is built in a 5’ to 3’ direction
• Directionality in the structure of the DNA molecule influences how it functions

Formation of Polynucleotides

The DNA Double Helix

The DNA Double Helix
• The two strands of the double helix are arranged in an antiparallel fashion, one of them going 5’-3’ and the other one going in the opposite direction

The “Backbone”
• Made up of alternating sugars and phosphates
• Connected by covalent bonds called phosphodiester linkages by dehydration reactions

The “rungs” of the Ladder
• Made up of nitrogenous bases
• Hydrogen bonded to each other
• The bases are hydrophobic and in their position inside the molecule they are shielded from the aqueous environment of the nucleus

Complimentary Base Pairing
• Each purine is bound to a pyrimidine
• A always to T (with 2 hydrogen bonds)
• C always to G (with 3 hydrogen bonds)
• Chargraff’s Rule: for any given species the % of Ts will by equivalent of the % of As while the % of Cs will be equivalent to the % of Gs

The DNA Double Helix

DNA vs. RNA
DNA
Number of Strands
Pentose Sugar
Nitrogenous Bases
RNA

Functions of DNA
• provides directions for its own replication
• directs RNA synthesis
• through RNA, controls protein synthesis (blueprints of the cell)

Function of Ribosomal RNA
• rRNA
• Together with proteins makes up the structure of the ribosomes, the site of protein synthesis

Function of Transfer RNA
• tRNA
• Recognizes the 3 base sequence on the messenger RNA and brings the appropriate amino acid to the ribosome fro protein synthesis

Function of Messenger RNA
• mRNA
• Carries the “code” from the DNA in the nucleus to the ribosome in the cytoplasm to instruct protein synthesis

Models of DNA Replication

Models of DNA Replication
• Conservative model- the two parent strands rejoin after acting as a template for new strands

Models of DNA Replication
• Semiconservative model- the new strands of DNA are made of one parental template strand, and one newly synthesized strand; this is the accepted model of DNA synthesis

Models of DNA Replication
• Dispersive Model- the DNA completely breaks down and the new DNA is made of a mixture of pieces of the parental and new DNA

DNA Replication
• What does the curriculum say?
• DNA polymerase
• Ligase
• RNA polymerase
• Helicase
• topoisomerase

The Origin of Replication
• Site where DNA synthesis begins
• In prokaryotes there is only one because the DNA is circular
• In eukaryotes there are several replication bubbles that eventually fuse

Enzymes involved in early DNA replication:
• Helicase- unzips and unwinds the DNA double helix
• Topoisomerase- relieves the tension further down the strand that is caused by the unwinding at the origin
• Single Strand Binding Protein- helps stabilize the single stranded DNA

The Energy Requirements of DNA
Synthesis
• Nucleoside
Triphosphate
• The triphosphate portion contains a lot of potential energy
• Two phosphates are removed and the energy that was held in the bonds is used for the polymerization of the new DNA

Synthesis of the Leading Strand
1.
The leading strand is synthesized continuously in the 5’ to 3’ direction; in the direction of the replication fork
2.
Primase- an enzyme that lays down an RNA primer on which the new DNA can be synthesized
3.
DNA Polymerase III adds new nucleotides to the 3’ end
4.
DNA Polymerase I removes the RNA primer and replaces it with DNA nucleotides
5.
DNA Ligase connects the DNA added by DNA Polymerase I with the remainder of the leading strand

Synthesis of the Leading Strand

Synthesis of the Lagging Strand
• DNA can only be synthesized in the 3’ to 5’ direction
• The lagging strand must be synthesized away from the replication fork; as the DNA unwinds, the lagging strand is synthesized in a series of small segments called Okazaki fragments

Synthesis of the Lagging Strand
1.
Primase lays down multiple RNA primers
2.
DNA Polymerase III adds new nucleotides until it reaches the next RNA primer
3.
DNA Polymerase I removes the RNA primers and adds DNA nucleotides in their place
4.
DNA Ligase connects the Okasaki fragments to make one continuous strand of DNA

Synthesis of the Lagging Strand

The DNA Replication Machine
• The various proteins that participate in DNA replication form one large complex
• The DNA replication machine is stationary and the DNA is fed through the machine like a thread through a needle
• In eukaryotic cells, multiple copies of the DNA machine are likely anchored in the nuclear matrix and copy multiple chromosomes at a time

Crash course

Proofreading
• Occurs simultaneously with replication
• DNA polymerase proofreads each nucleotide against the template and when mistakes are found, it fixes them

Nucleotide Excision Repair
• Nuclease- enzyme that cuts out problems in the DNA
• DNA polymerase replaces the excised nucleotides with good ones
• DNA ligase joins the nucleotides to the existing strand

Erosion of Gene Coding DNA and Aging
• The problem with the lagging strand in eukaryotic DNA
• DNA polymerase can only add nucleotides to the 3’ end
• After the primer at the end of the lagging strand is removed,
DNA polymerase cannot add new nucleotides
• THE PROBLEM: eventually this would erode some of the genes coded for in the DNA

Erosion of Gene Coding DNA and Aging

The Solution: Telomers
• Short repeating segments of DNA that do not contain genes, but multiple repetitions of one short nucleotide sequence
• The protect the organisms genes from being eroded by successive rounds of DNA replication
• Telomers do not prevent DNA shortening, but do postpone the erosion of genes

Telomerase
• Enzyme that catalyzes the lengthening of telomers in eukaryotic germ cells (what are germ cells???)
• Telomerase is not active in most cells but is active in the germ cells of zygotes