Unit 6 (DNA and RNA Structure + DNA Replication)

Rosalind Franklin discovery

• DNA has a regular and repetitive pattern

• Found through an X-ray crystallography

Edwin Chargaff discovery

• Amount of adenine = amount of thymine

• Amount of cytosine = amount of guanine

Purines

Double ring structure (A, G)

Pyrimidines

Single ring structure (C, U, T)

Nucleotide pairing

• Base pairs are held together by hydrogen bonds

• Adenine and thymine have two hydrogen bonds

• Cytosine and guanine have three hydrogen bonds

• Hydrogen bonds allow for the DNA strands to be easily separated during replication

DNA structure

1. Double stranded

• Backbone: sugar-phosphate

• Canter: nucleotide pairing

2. Antiparallel

• One strand runs 5’→3’ and the other runs 3’→5’

• 5’ end: free phosphate group

• 3’ end: free hydroxyl group

Key functions of DNA

Primary source of heritable information

• Genetic information is stored in and passed from one generation to the next through DNA

• Exception: RNA is the primary source of heritable information in some viruses

Eukaryotic DNA

• Nucleus

• Linear chromosomes

Prokaryotic DNA

• Nucleotide region

• Circular chromosomes

Plasmids

Small, circular DNA molecules that are separate from the chromosomes

• Plasmids replicate independently from the chromosomal DNA

• Primarily found in prokaryotes (some eukaryotes)

• Contains useful genes, but not required for survival

Plasmid manipulation

• Can occur in labs

• Plasmids can be removed from bacteria, and then a gene of interest can be inserted into the plasmid to form a recombinant plasmid DNA

• When the recombinant plasmid is inserted back into the bacteria, the gene will be expressed

• Bacteria can exchange genes found on plasmids with neighboring bacteria

• Once the DNA is exchanged, the bacteria can express the genes acquired

• Helps with the survival of prokaryotes

RNA vs DNA

• RNA: ribonucleic acid, single stranded, A=U and C=G

• DNA: deoxyribonucleic acid, double stranded, A=T and C=G

DNA replicaiton

• S phase of the cell cycle

• 3 alternative models: conservative, semi-conservative, dispersive

Conservative Model

• The parental strands direct synthesis of an entirely new double stranded molecule

• Parental strands are fully “conserved”

• One exact copy and one entirely different copy

Semi-conservative model

• The two parental strands each make a copy of itself

• After one round of replication, the two daughter molecules each have one parental and one new strand

• The correct model

Dispersive model

• The material in the two parent strands is dispersed randomly between the two daughter molecules

• After one round of replication, the daughter molecules contain a random mix of parental and new DNA

DNA replication: Step 1

• Begins at sites called origins of replication

• Various proteins attach to the origin of replication and open the DNA to form a replication fork

DNA Replication: Step 2

• Helicase will unwind the DNA strands at each replication fork

• To keep the DNA from re-bonding with itself, proteins called single-strand binding proteins (SSBPs) bind to the DNA to keep it open

• Topoisomerase will help prevent strain ahead of the replication fork by supercoiling

DNA Replication: Step 3

• Primase initiates replication by adding short segments of RNA, called primers, to the parental DNA strand

• The enzyme that synthesizes DNA can only attach new DNA nucleotides to an existing strand of nucleotides

• Primers serve as the foundation for DNA synthesis

DNA Replication: Step 4

• Antiparallel elongation

• DNA Polymerase III (DNAP III) attaches to each primer on the parental strand and moves in the 3’ to 5’ direction

• As it moves, it adds nucleotides to the new strand in the 5’ to 3’ direction

• The DNAP III that followers helicase is known as the leading strand and requires only 1 primer

• The DNAP III on the other parental strand that moves away from helicase is known as the lagging strand and requires many primers

DNA Replication: Step 5

• The leading strand is synthesized in one continuous segment, but since the lagging strand moves away from the replication fork, it is synthesized in chunks

• Okazaki fragments: segments of the lagging strand

DNA Replication: Step 6

• After DNAP III forms an Okazaki fragment, DNAP I replaces RNA nucleotides with DNA nucleotides

• DNA Ligase: joins the Okazaki fragments, forming a continuous DNA strand

Problems at 5’ end

• Since DNAP III can only add nucleotides to the 3’ end, there is no way to finish replication on the 5’ end of a lagging strand.

• Over many replications, the DNA would become shorter and shorter

• Can protect the genes on DNA with Telomeres: repeating units of short nucleotide sequences that do not code for genes

• Form a cap at the end of the DNA to help postpone erosion

• Adds telomeres to DNA

Proofreading and repair

• As DNA polymerase adds nucleotides to the new DNA strand, it proofreads the bases added

• If error still occur, mismatch repair will take place → enzymes remove and replace the incorrectly paired molecule

• If segments are damaged, nuclease can remove segments of nucleotides and DNA polymerase and ligase can replace the segments