chapter 5 - dna and chromosomes

chemical basis of genes

• building blocks of dna

• double stranded

• double helix

building blocks of dna

• phosphate backbone + base → nucleotide

• sugar phosphate backbone + hydrogen bonded base pairs → double stranded helix

• 5’ → 3’

first key experiment leading to identification of dna as genetic material

• frederick griffith - studied streptococcus pneumococcus pathogenicity, showing that material could be transferred from a heat killed virulent strain to a non virulent strain making the non virulent strain virulent

• the process of transformation

key idea 1 - demonstrating that dna is transforming principle

• a mixture of things has an effect on something

• separate the components, see which one has the effect

key idea 2 - demonstrating that dna is transforming principle

• a mixture of things has an effect on something

• delete components one by one, see which deletion cause the effect to disappear

hershey chase experiment

• some phage viruses contain dna and protein, when they infect bacteria, the bacteria make more viruses, so something in the virus has genetic information

• electron microscopy showed that the virus attaches to the bacteria, and injects something into it

• label phage dna with P³² and phage proteins with S³⁵ then infect bacteria, let the injection occur, then tear off the virus and see what got injected into the bacteria

chargaffs rule

• complementary base pairing

• base composition varies significantly between species

• it did not matter from which tissue or organ the dna came from, base composition was constant within the species

• A=T and C=G - present in equimolar amounts

  • A=T does not equal to C=G

structure of dna

• 1953 watson and crick used molecular models based on x ray diffraction data from franklin and wilkins to propose a double helical structure for dna where the helix was held together by A-T and C-G base pairs

properties of dna double helix

• two dns strands wrapped in a right handed helix

• two chains are antiparallel

• sugar phosphate backbone on the outside, bases project toward the center

• the bases are stacked one on top of the other

  • hydrophobic interactions and van der waals forces stabilize the helix

complementary base pairing

• purine/pyrimidine base pairs

• A - T

  • 2 H bonds

  • less stable than g-c

• G-C

  • 3 H bonds

  • more stable than a-t

properties of dna double helix - nucleotide

• h bonds between the bases contribute to helical stability

• helix diameter is uniform because pase pairs have identical widths

• 10 bases per helical turn

• spaces between the turns of the helix forms major and minor grooves

  • important sites for dna/protein interactions

• complementarity - nucleotides on one chain are complementary to nucleotides on the other strand

implications of watson crick model

• linear arrangement of nucleotides could store the genetic information

• complementarity provided a mechanism for replication of genetic information

• how genetic info was expressed was still unknown 

central dogma of molecular biology

replication makes dna → transcription makes rna → translation makes protein

genome

• the total dna complement of an organism

• the more complex an organism, the larger its genome

• the complete genomes of many organisms, including humans, have been sequenced

• bioinformatics tools are now used to identify and count genes in sequences genomes

• genome can be haploid, diploid, or polyploid

genomic dna is packaged into chromosomes

• chromosomes - long, single dna molecules associated with proteins that fold and pack the dna into a compact structure

  • 10,000 fold compaction

chromatin

a complex of dna and associated proteins

the organization of dna in chromosomes must be _

dynamic

cell cycle

interphase = G1 + S + G2

chromosomes during interphase and mitosis

interphase chromosomes are organized within the _

• nucleus

• is 1000 fold less compact than metaphase chromosomes

_ are the basic units of eukaryotic chromatin structure

• nucleosomes

• bacteria dont have nucleosomes - they have a big piece of circular dna that is compacted by various proteins

_ form the nucleosomal core

histone octamers

properties of histones

• 5 histones

• positively charged

• evolutionary conserved

• one nucleosome

properties of histones - 5 histones

• nucleosome core

  • H2A

  • H2B

  • H3

  • H4

• required for 30 nm fiber packing level

  • H1

properties of histones - positively chraged

rich in lysine and arginine

properties of histones - evolutionary conserved

bovine and pea H4 differ by only 2 aa

properties of histones - one nucleosome

146 bp DNA fragment + 2 H2A, 2 H2B, 2 H3, and 2 H4 (histone octamer)

dna vs protein in nucleosome

levels of chromosomal prganization

chromatin remodeling complexes alter chromatin structure

modification of _ tails also alters chromatin structure

modification of histone n-terminal tails