The Structure and Function of Macromolecules Chapter 5 2 – Nucleic Acids

Macromolecules: The Molecules of Life Carbohydrates Nucleic Acids Proteins Lipids

The Structure of Nucleic Acid Monomers Nucleotide -- nitrogenous base, a pentose sugar, and a phosphate group Nucleoside -- portion of a nucleotide without the phosphate group

FIGURE 3-24 Deoxyribose nucleotide

Nucleotide Monomers There are two families of nitrogenous bases: Pyrimidines have a single six-membered ring Purines have a six-membered ring fused to a five-membered ring

Nitrogenous base Phosphate group Pentose sugar Nitrogenous bases Pyrimidines Purines Pentose sugars Cytosine C Thymine (in DNA) T Uracil (in RNA) U Adenine A Guanine G Deoxyribose (in DNA) Nucleoside components Ribose (in RNA) 5¢ end 3¢ end Nucleoside Nitrogenous base Phosphate group Nucleotide Polynucleotide, or nucleic acid Pentose sugar

Purines vs Pyrimidines King CUT lives in a Pyramid! CUT = Cytosine, Uracil, Thymine Cytosine, Uracil, Thymine are Pyrimidines Pyrimidines are CUT from Purines Pyrimidines are single-ring compounds, Purines are double ring compounds

Non-polymer Nucleotides not large molecules or polymers Intracellular messengers Energy carriers Enzyme assistants

Other Nucleotides Nucleotides as intracellular messengers Cyclic nucleotides (e.g. cyclic AMP) carry chemical signals between molecule

Other Nucleotides Nucleotides as energy carriers Adenosine triphosphate (ATP) carries energy stored in bonds between phosphate groups

NAD+: Nicotinamide Adenine Dinucleotide Vitamin B3

NADP+: Nicotinamide Adenine Dinucleotide Phosphate

FAD: Flavin Adenine Dinucleotide

Other Nucleotides Nucleotides as enzyme assistants Coenzymes help enzymes promote and guide chemical reactions

Nucleotide Polymers Nucleotide monomers – build polynucleotide Covalent bonds –OH group on the 3´ carbon of one nucleotide phosphate on the 5´ carbon on the next Backbone of sugar-phosphate units nitrogenous bases as appendages

LE 5-26a Nucleoside Nitrogenous base Phosphate group Pentose sugar 5¢ end Nucleoside Nitrogenous base Phosphate group Pentose sugar Nucleotide 3¢ end Polynucleotide, or nucleic acid

Nucleotide Polymers DNA antiparallel Two types: DNA makes more DNA Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA antiparallel Backbones in opposite 5´ to 3´ directions DNA makes more DNA DNA directs synthesis of messenger RNA (mRNA) mRNA controls protein synthesis Occurs in ribosomes

DNA vs RNA Pyrimidine in DNA is Thymine; RNA uracil DNA is double-stranded; RNA single In DNA, the sugar is deoxyribose; in RNA ribose Pyrimidine in DNA is Thymine; RNA uracil DNA directs hereditary information; RNA directs protein synthesis DNA is DNA; RNA comes in 3 forms messenger RNA (mRNA)– protein structure from DNA to ribosome ribosomal RNA (rRNA) – makes up ribosomes transfer RNA (tRNA) – carries amino acids to the ribosome/mRNA

Types of RNA DNA is DNA; RNA comes in 3 forms …. not exactly! messenger RNA (mRNA)– protein structure from DNA to ribosome ribosomal RNA (rRNA) – makes up ribosomes transfer RNA (tRNA) – carries amino acids to the ribosome/mRNA …. not exactly! http://en.wikipedia.org/wiki/List_of_RNAs

DNA Most celebrated molecule of our time Hereditary information Sugar–phosphate backbone 5 end Nitrogenous bases Thymine (T) Adenine (A) Cytosine (C) DNA nucleotide Phosphate 3 end Guanine (G) Sugar (deoxyribose) DNA Most celebrated molecule of our time Hereditary information Directs the development of biochemical, anatomical, physiological, and (to some extent) behavioral traits

Variation and Diversity Slight differences between closely related individuals Distantly related individuals – greater differences © 2009 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 4/e

The Search for Genetic Material It needed to: Contain information Be easy to copy Be variable, to account for diversity

DNA or Protein? Nucleic Acids Proteins First isolated 1869 -- Friedrich Miescher Proteins Recognized in 18th C. First described -- Gerardus Johannes Mulder Named -- Jöns Jacob Berzelius in 1838.

DNA or Protein? Thomas Hunt Morgan – 1911 Chromosomes carried genes Composed of DNA and protein Which is the genetic material? Protein is large, complex, and stores info DNA seemed too small and unlikely

Griffith Experiment -- 1928 Transformation of one strain by another Two strains of bacteria R—harmless S—deadly Heat‑killed S is also harmless Heat‑killed S makes R deadly

Avery, MacLeod, & McCarty 1944 Used the same assay system Isolated compounds from Strain S Added these to Strain R Only DNA transformed Strain R

Additional Evidence 1947 -- Erwin Chargaff: DNA composition varies from one species to the next Makes DNA more credible By 1950s -- DNA composition known but not structure

Hershey and Chase -- 1952 Phage head Tail Tail fiber 100 nm DNA LE 16-3 Hershey and Chase -- 1952 Phage head Tail Tail fiber 100 nm DNA Bacterial cell

Hershey and Chase -- 1952 DNA, not protein, is genetic material

Franklin’s X-ray diffraction photograph of DNA LE 16-6 Rosalind Franklin Franklin’s X-ray diffraction photograph of DNA

Watson & Crick Determined the 3D structure of DNA Structure revealed its function Franklin’s X-ray crystallographic studies Double helix Ladder twisted into a spiral coil Uniform diameter

Purine + purine: too wide LE 16-UN298 Purine + purine: too wide Pyrimidine + pyrimidine: too narrow Purine + pyrimidine: width consistent with X-ray data

Base-Pairing Rules Strands held together by hydrogen bonds Strict base-pairing rules followed Purine to Pyrimidine A binds to T G binds to C Makes copying sequence possible

LE 5-27 5¢ end 3¢ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 5¢ end New strands 3¢ end 5¢ end 5¢ end 3¢ end

FIGURE 9-6 Basic features of DNA replication During replication, the two strands of the parental DNA double helix separate. Free nucleotides that are complementary to those in each strand are joined to make new daughter strands. Each parental strand and its new daughter strand then form a new double helix.

DNA Structure Explains Function Easily copied Each strand is a template for the other DNA sequence is information Information contained in the order of the four bases Millions of bases in length Accounts for diversity Alleles have different DNA sequences

Replication Models Meselson & Stahl (1958) Conservative model. The two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix. Semiconservative model. The two strands of the parental molecule separate, and each functions as a template for synthesis of a new, comple-mentary strand. Dispersive model. Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA. Parent cell First replication Second Replication Models Meselson & Stahl (1958) Labeled strand -- heavy isotope of nitrogen Labeled free nucleotides -- lighter isotope of nitrogen

LE 16-11 Bacteria cultured in medium containing 15N Bacteria transferred to medium containing 14N DNA sample centrifuged after 20 min (after first replication) DNA sample centrifuged after 40 min (after second replication) Less dense More dense First replication Second replication Conservative model Semiconservative model Dispersive model

DNA Replication: A Closer Look Quick and accurate More than a dozen enzymes and other proteins participate

Replication Origins of Replication Eukaryotic chromosome -- hundreds to thousands Replication proceeds in both directions Replication fork – ends of each replication bubble

LE 16-12 Parental (template) strand 0.25 µm Origin of replication Daughter (new) strand Bubble Replication fork Two daughter DNA molecules In eukaryotes, DNA replication begins at may sites along the giant DNA molecule of each chromosome. In this micrograph, three replication bubbles are visible along the DNA of a cultured Chinese hamster cell (TEM).

DNA Replication DNA Polymerase Many enzymes and proteins are involved Catalyze elongation at a replication fork Many enzymes and proteins are involved Initiate replication Unwind the DNA Stabilize the open strands Connect bases -- nucleoside triphosphate Process takes about 8 hours in humans

LE 16-13 New strand Template strand 5¢ end 3¢ end 5¢ end 3¢ end Sugar Base Phosphate DNA polymerase 3¢ end 3¢ end Pyrophosphate Nucleoside triphosphate 5¢ end 5¢ end

Antiparallel Elongation The antiparallel structure of the double helix (two strands oriented in opposite directions) affects replication DNA polymerases add nucleotides only to the free 3end of a growing strand DNA elongates only in the 5 to  3direction

The DNA Replication Machine Complex -- probably stationary DNA polymerase “reels in” parental DNA “extrude” daughter DNA