Understanding DNA

Biology 12

Ms. Bowie

Understanding DNA

• DNA stands for deoxyribonucleic acid

• DNA is the genetic material. – transfer from parent cell to daughter cell and – from parent organism to offspring.

• The 3 main components of DNA are:

Understanding DNA

A Nucleotide of DNA

• There are four nitrogenous bases in DNA.

– Adenine (A),

– Guanine (G)

– Thymine (T)

– Cytosine (C)

– Uracil (U)

The Nitrogenous Bases

which are double ringed which are double ringed purinespurines(Hint: “pure” = (Hint: “pure” = AAlways lways GGood)ood)

which are single ringed which are single ringed pyrimidinespyrimidines(Hint : “pyro” = (Hint : “pyro” = TTake ake CCare)are)

found in RNA instead of found in RNA instead of thyminethymine

http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&docid=6VK_cpVpQLuC8M&tbnid=t8lThd73QsV5fM:&ved=0CAYQjRw&url=http://www.bio.miami.edu/dana/250/250S11_7.html&ei=D64lU5DMI6OP0gGSsIGIBQ&psig=AFQjCNH9Oc6Z2t149nWQlZhDEIxdxCVIQw&ust=1395064627635887

• DNA is made of polymers of many nucleotides held together by phosphodiester bonds between the phosphate group and the adjacent sugars.

• Nitrogenous bases are held together by hydrogen bonds. Two between A & T and Three between C & G

Bonds in DNA

• Erwin Chargaff determined that: – Adenine always pairs with Thymine

– Cytosine always pairs with Guanine

Chargaff’s Rule

Numbering Carbons in the Ring

• Carbons are numbered clockwise, starting with the carbon atom to the immediate right of the oxygen atom.

• The first one would be called 1’, the next would be 2' (2 prime)...

• The nitrogenous base attaches to the sugar at the 1' location (via a glycosyl bond).

• The phosphate group attaches to the sugar at the 5' location (via an ester bond).

The Race for DNA

• Linus Pauling – building ball and stick models

using his expertise in chemistry.

• He proposed 1 model– it did not show how copying of

the DNA could occur.

• His son, Peter Pauling, went to work with another group in Cambridge, England.

The Race for DNA• Rosalind Franklin and Maurice Wilkins

– King's College in London – studies using the diffractions with X-ray

crystallography. – Work was based on serious scientific evidence,– They have great difficulty working TOGETHER.– Franklin uncovered the shape of DNA when she

found an x-ray diffraction in a cross pattern. – Wilkins shared this data with Watson who used it to

further his own work.

The Race for DNA• James Watson and Francis Crick

– considered lazy slackers

– neglected experimentation and evidence

– focused on the structure of DNA using 3D modelling

– when Wilkins showed the x-pattern of Franklin's x-ray diffraction, he immediately knew what the structure might look like.

– They came up with the modern structure of DNA that accurately answered the question as to how DNA can create perfect copies of itself.

The Race for DNA

• Watson, Crick and Wilkins won Noble Prizes for their Discovery of the structure of DNA.

• However, Franklin did not receive one as she died before the awards were given.

DNA Double Helix Structure

• DNA is made of 2 antiparallel strands of nucleotides.

• It is important to be able to identify the 3' and 5' ends of each strand.

DNA Double Helix Structure

• Thanks to Chargaff's Rule, we only state the 5' to 3' strand, since the complementary strand can be easily deduced.

5' - GCAATCTA - 3'3' - CGTTAGAT - 5'

Replicating DNA

• DNA must be copied in order for single cells to be replaced as they age or are damaged.

• It also happens so organisms can grow.This process is known as mitosis.

Replicating DNA

• Semiconservative: each DNA molecule is made of one parent strand and one newly synthesized strand.

• Conservative: each DNA molecule reforms so that both new strands stay together and both parent strands stay together.

• Dispersive: where bits and pieces of the parent and new strands are interspersed in both strands following the replication.

Replicating DNA

The Process of Replicating DNA• The two DNA strands separate

• Each strand serves as a template

• DNA replication begins at the origin of replication.

The Process of Replicating DNA

• DNA replication begins at the origin of replication.

The Process of Replicating DNA

• Replication proceeds (following the AT/CG rule) outward from the origin in opposite directions.

• This is a process called bidirectional replication.

• In simple bacteria, which have a small circular chromosome, there is a single origin of replication.

The Process of Replicating DNA

• The origin of replication forms a bubble that creates two DNA replication forks.

• Replication begins near the opening of each fork.

The Process of Replicating DNA

• The building of the new DNA always begins with a primer.

• New DNA is always built in the 5' to 3' direction.

The Process of Replicating DNA

• One strand will be the leading strand. The other will be the lagging strand.

• The leading strand moves in the same direction as the fork is moving.

• The leading strand is replicated as one long continuous molecule.

The Process of Replicating DNA

• The lagging strand is made in a series of small fragments which will eventually form a continuous strand.

• Synthesis of this strand goes in the direction away from the fork.

• These fragments are known as Okazaki fragments.

DNA Replication ProteinsStep 1: Formation and Movement of the Replication ForkStep 1: Formation and Movement of the Replication Fork

DNA Replication ProteinsStep 1: Formation and Movement of the Replication ForkStep 1: Formation and Movement of the Replication Fork

DNA Replication Proteins

» In prokaryotes, 3- 5 enzymes that serve to replicate and repair the DNA strand. These are DNA polymerase I, II, III, IV & V.

» In eukaryotes, there are 12+ DNA polymerases involved.

Step 2: Synthesis of the Leading and Lagging StrandsStep 2: Synthesis of the Leading and Lagging Strands

DNA Replication Proteins

» As DNA polymerase III slides along the DNA, free nucleotides with 3 phosphate groups, called deoxynucleoside triphosphates, hydrogen bond to the exposed bases in the template strand according to the AT/GC rule. DNA polymerase III breaks the bond between the 1 and 2nd phosphate groups releasing a pyrophosphate (2 phosphate groups, which are recycled.

»

Step 2: Synthesis of the Leading and Lagging StrandsStep 2: Synthesis of the Leading and Lagging Strands

DNA Replication Proteins

» DNA polymerase III can't polymerize a DNA strand unless a DNA or RNA strand is already attached to the template.

» An enzyme called DNA primase is needed if the template is bare. DNA primase makes a complimentary primer that is actually a short segment of RNA, usually about 10-12 nucleotides long. At a later stage in replication, the RNA primer is removed and replaced with DNA by DNA Polymerase I.

Step 2: Synthesis of the Leading and Lagging StrandsStep 2: Synthesis of the Leading and Lagging Strands

DNA Replication Proteins

» DNA polymerase can only synthesize new DNA in the 5' to 3' direction (of the new strand).

» The Okazaki fragments must be linked together (bonded) on the lagging strand.

» This bond is reformed by an enzyme known as DNA ligase.

Step 2: Synthesis of the Leading and Lagging StrandsStep 2: Synthesis of the Leading and Lagging Strands

DNA Replication Proteins

• There are many other proofreading enzymes known as exonucleases that correct and repair mistakes in the newly forming DNA strands.

• If they detect a mismatched pair, they will backtrack, cut it out and replace it with the correct pair.

• If the repairs are done immediately to avoid being copied in the next replication. Mistakes that make it through can result in mutations.

Step 3: Proofreading and Repair of newly formed DNA strandsStep 3: Proofreading and Repair of newly formed DNA strands

DNA Replication ProteinsStep 3: Proofreading and Repair of newly formed DNA strandsStep 3: Proofreading and Repair of newly formed DNA strands

• http://www.wiley.com/college/pratt/0471393878/instructor/animations/dna_replication/index.html

• http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter3/animation__dna_replication__quiz_1_.html

• http://www.johnkyrk.com/DNAreplication.html