Molecular Biology Molecular Biology The study of DNA

Molecular Biology

Molecular Biology • The study of DNA and how it serves as a chemical basis of heredity

DNA and RNA • Nucleic acids • Polymers of nucleotides called polynucleotides • Nucleotides (monomers) are made up of – – Nitrogenous base – Adenine, Thymine (Uracil), Cytosine, Guanine – 5 -carbon sugar (pentose) – Phosphate group • Nucleotides are joined together by covalent bonds between the sugar of one nucleotide and the phosphate of another nucleotide – This forms a sugar-phosphate backbone • Nitrogenous bases extend from the sugar-phosphate backbone

Sugar-phosphate backbone Phosphate group Nitrogenous base Sugar DNA nucleotide Phosphate group Nitrogenous base (A, G, C, or T) Thymine (T) Sugar (deoxyribose) DNA nucleotide DNA polynucleotide

• Sugars – ▫ DNA – deoxyribose ▫ RNA – ribose • Nitrogen Bases ▫ Can be divided into Purines - larger; double rings Adenine and Guanine Pyrimidines – single structure rings Thymine, cytosine, uracil

Nitrogenous base (A, G, C, or T) Phosphate group Thymine (T) Sugar (deoxyribose)

Nitrogenous base (A, G, C, or U) Phosphate group Uracil (U) Sugar (ribose)

Thymine (T) Cytosine (C) Pyrimidines Guanine (G) Adenine (A) Purines

Uracil Adenine Guanine Cytosine Phosphate Ribose

Structure of DNA • James D. Watson and Francis Crick deduced the secondary structure of DNA, with X-ray crystallography data from Rosalind Franklin and Maurice Wilkins • DNA is made up of two polynucleotide chains joined together by hydrogen bonding between bases, twisted into a helical shape • This is known as a double helix! • The sugar-phosphate backbone is on the outside • The nitrogenous bases are perpendicular to the backbone in the interior • They act like the rungs of the ladder

Twist

The two DNA strands are antiparallel to each other (facing opposite way) Hydrogen bond Base pair Ribbon model Partial chemical structure Computer model

Structure of DNA • Chargaff’s rule That the nitrogenous bases have complimentary bases • Specific pairs of bases give the helix a uniform shape – A pairs with T, forming two hydrogen bonds – G pairs with C, forming three hydrogen bonds • What would be complementary to CAGGATTCAGTACCG ?

Hydrogen bond Base pair Ribbon model Partial chemical structure Computer model

DNA Replication

Process • Both the strands of DNA separate from each other and act as templates for new strands of DNA to be made • They use the base pairing rule and enzymes to do this. • The daughter DNA is complementary to the parent DNA • Semiconservative model – each strand of the DNA is made up of an old and new strand of DNA

Meselson and Stahl • Did an experiment to prove that replication is semiconservative

Parental molecule of DNA

Nucleotides Parental molecule of DNA Both parental strands serve as templates

Nucleotides Parental molecule of DNA Both parental strands serve as templates Two identical daughter molecules of DNA

DNA Replication • Happens in both directions at many sites simultaneously on both strands • DNA replication begins at the origins of replication – These sites have specific DNA sequences of nucleotides – Proteins attach here and help the DNA unwind at the origin – This produces a “bubble” – Replication proceeds in both directions from the origin – Replication ends when products from the bubbles merge with each other

Origin of replication Parental strand Daughter strand Bubble Two daughter DNA molecules

DNA Replication • Each strand of DNA has a 5’ and a 3’ end The 5’ and 3’ refer to the carbon number on the sugar The 3’ end has an OH The 5’ end has a Phosphate • The strands are opposite of each other

3 end 5 end P 4 3 P 5 2 1 2 3 1 4 5 P P P 3 end 5 end

DNA Replication • DNA replication occurs in the 5’ 3’ direction – This is because DNA polymerase can only add nucleotides on in the 3’ direction because of the OH – The daughter strand can only grow in the 5’ to 3’ direction – Replication is continuous on the parent 3’ 5’ template – Replication is discontinuous on the parent 5’ 3’ template, forming short segments (Okazaki fragments)

Proteins that help with Replication • Helicase- an enzyme that helps to unwind the DNA strands. Creates replication fork. • SSBs – Keep the two strands of DNA apart • RNA Primase – Attaches an RNA primer to the template • DNA polymerase – helps to add nucleotides and proofreads DNA as well as removes mismatched pairs • RNAase H – Removes the RNA primer • Ligase – the glue that connects Okazaki fragments

DNA polymerase molecule 5 3 3 5 Parental DNA 3 5 Daughter strand synthesized continuously Daughter strand synthesized in pieces 5 3 DNA ligase Overall direction of replication DNA Replication Animation