Lecture 13

Textbook Reading

4.2 DNA Structure and Function

• sugar-phosphate backbone, made up of deoxyribose sugar and phosphate groups

• in a give DNA molecule:

  • number of purine = number of pyramidines

  • has an equal number of T’s and A’s, and equal number of C’s and G’s

• helical in nature: repeated distances (0.34 nm, 2.0 nm, 3.4 nm)

• two stands of DNA with sugar-phosphate backbones on outside, bases on inside, forming purine-pyramidine pairs: A=T, G≡C (complementary base pairing)

  • purines: A, G (6 + 5 membered rings)

  • pyramidines: T, C (6 membered rings)

  • 3 hydrogen bonds between G≡C makes G-C pairs slightly stronger

• one strand runs 5’→3’, one strand runs 3’→5’ (antiparallel)

• forms a double helix due to bases’ carbon-nitrogen rings being mostly nonpolar

The Tertiary Structure of DNA

• supercoils — when DNA is wound too tightly or loosely with respect to the number of base pairs per helical turn, it can twist on itself

• DNA in eukaryotes/certain archaea will form 3º structures by wrapping around specialized DNA-binding proteins called histones

DNA Contains Information

• DNA’s primary structure serves as a template for synthesis of a complementary strand

  1. two strands get separated by breaking hydrogen bonds through heat or enzymes

  2. free deoxyribonucleotides form H-bonds with complementary bases on the original (template) DNA strand, and form a 5’→3’ (opposite) complementary strand with phosphodiester linkages

  3. complementary base pairing produces two identical daughter DNA molecules

4.3 RNA Structure and Function

RNA Structure

• primary structure

  1. sugar in RNA is ribose (with the added hydroxyl group, it’s much more reactive and less stable)

  2. thymine is replaced by uracil

• secondary structure

  • purine/pyramidine hydrogen bond with complementary bases on the same strand (forms an antiparallel helix)

• tertiary structure

  • pseudoknot structures

RNA’s Function

• RNA is intermediate between DNA and protein

  • messenger RNA transmits info needed to synthesize polypeptides

• ribozymes — RNA enzymes that catalyze reactions similar to protein enzymes

15.1 What are Genes Made of?

• DNA, not protein, is the hereditary material

• each deoxyribonucleotide has a deoxyribose sugar, phosphate group, and a nitrogenous base

• deoxyribonucleotides form polymers by forming a phosphodiester linkage between hydroxyl group at 3’ carbon of one deoxyribose and the phosphate group of the 5’ carbon on another deoxyribose

• DNA is 5’→3’ with an exposed phosphate group at 5’ end and exposed -OH group at 3’ end

Lecture Slides

Central Dogma

• DNA encodes the genetic information that directs the cell how to make proteins and RNAs

• information carried in our genes does not pass directly from DNA ot proteins

• instead, the information carried in the nucleotide sequence of our genes is first copied into an RNA intermediate (transcription)

• the nucleotide sequence information in the RNA is then used to build proteins (translation)

• the flow of genetic information from DNA to RNA to Protein is referred to as the Central Dogma of Molecular Biology

Discovering the function of DNA

• by 1940s, hereditary material known to reside on one or more chromosomes

• chromosomes are composed of chromatin, which is a complex of DNA and protein

• we know proteins were made of 20 amino acids, and DNA was made of 4 nucleotides

Discovering the structure of DNA

• chargaff’s rules

  • amount of each dNTP varies between organisms, but

  • [dA] = [dT] and [dC] = [dG] in ALL organisms

• rosalind franklin and maurice wilkins

  • x-ray diffraction suggested helix of two strands, with a uniform width that stacks bases, with sugar-phosphate on outside

• james watson and francis crick

  • created a scale model that fit all available data

DNA

• if DNA contains more than one chain of nucleotides, what forces hold them together

  • if it’s hydrogen bonds forming between a purine on one strand and a pyrimidine on the other

    • explains uniform width (2 nm) and chargaff’s rules

• if purines are opposite pyrimidines

  • only G can “fit” opposite C and A opposite T in order for groups to be precisely positioned for hydrogen bonds to form between them

    • called watson-crick or complementary base pairing

• double-stranded DNA is antiparallel and complementary

• the information content of DNA resides in the sequence of its bases

  • only have 4 to choose from

  • but, potential for different combinations is staggering when the size of chromosomes is considered (4^n possibilities)

• watson and crick’s model of DNA double helix

  • placed a great deal of importance on complementary bases

  • suggested a copying mechanism

    • each DNA strand in a double helix contains all the information needed to make a new identical double helix

  • if “parental” double helix is unwound, all that is necessary to build 2 identical “daughter” helices is to add complementary bases to the now-single-stranded DNA chains (templates)

• How are the parent strands maintained?

  • conservative vs semi-conservative vs dispersive

  • semi-conservative makes the most sense

• order of events for dna replication

  1. determine where to start

  2. separate the strands

  3. “prime the pump”

  4. synthesize DNA

  5. clean up

• the “start signal” for DNA replication is the origin of replication (ori for short)

  • ori is a specific sequence of bases in the DNA

  • strands will be separated at the ori, and synthesis of new DNA will occur from both parent strands in both directions away from the ori, creating a replication bubble