DNA structure Flashcards
what’s DNA made up of
-nucleotides
-they have 5’-3’ polarity
-in nucleotide: triphosphate (when 3 phosphates are present), deoxyribose sugar, base
-can have nucleoside monophosphate, diphosphate and triphosphate
bonds in DNA
-phophodiester linkage between two nucleotides
-joined by covalent bonds
what was the Experiment by Erwin Chargaff
-Inspired by reading Avery et al’s paper showing that DNA transforms bacteria.
-Used paper chromatography to separate and isolate the nucleobase components of DNA from a number of species
-he composed different proportions of bases
what were Chargaff’s rules
-%A = %T and %G = %C
Or, % purines = % pyrimidines
-%AT =/= %GC.
-Composition varies from one species to another: some species are more “AT-rich” than others.
what’s X-ray crystallography structure of DNA
-solution of molecules (as pure as possible) and evenly spaced
-x ray shone into this solution through a lead screen- lead screen blocks x-ray in various ways and refracts the x-ray
-once x-ray shone through the lead screen through the solution it hits a photograph plate where there is an even pattern of spots caused by x-rays are interrupted by the screen
what’s the X-ray crystallography structure of DNA
-spiral shape
-even spacing- even structure
-one turn of the helix known by measuring how far DNA molecules are from one another
-Regular pattern –> repeating, even structure
what information did James Watson and Francis Crick have for their model model
-Structures of the nucleotides
-Ratios of the different nucleotides in the DNA molecule
-Crystal structure
what were the Main features of Watson and Crick’s model
-A-T and G-C hydrogen-bonded base pairs
-Antiparallel strands
-Right-handed double helix
-One helical turn every 10.5 bp
-Major and minor grooves
H-bonding between a purine and a pyrimidine
-H bonding in water where the H is slightly +ve and the O is slightly -ve
-water is polar which causes the attraction between the oppositely charged particles
what does One purine and one pyrimidine maintain
-the width of the DNA molecule
-Mispairing between two purines or two pyrimidines would cause distortion in the DNA molecule
-2 pyrimidines= DNA too skinny
-2 purines= DNA to wide
-1 pyrimidine and 1 purine= DNA width is consistent with x-ray data (gap between these 2 is the length of the H bond)
purine structure
-2 carbon rings
-with 2 H bonds: adenine
-with 3 H bonds: guanine
pyrimidines structure
- 1 carbon ring
-2 H bonds: thymine
-3H bonds: cytosine
what occurs with Antiparallel, complementary DNA strands
-5’-3’ polarity where the phosphate is attached to the carbon 5’ and the OH group is attached to the carbon 3’
-5’-3’ are running in opposite directions hence why they’re antiparallel
what’s the Double helical structure
-Right-handed helices
-Each phosphate backbone forms a helix – so, “double”
-antiparallel strand twisting around one another- called a double helix
whats the Major and minor groove in the DNA double helix
major groove: bigger bit vice versa- look at slide 18 if confused
whats the Structural elements of chromosomes and plasmids
-Wikipedia definition of chromosome: “a long DNA molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones […]”
-Remember Sutton and Boveri showing that chromosomes contained genes along their length.
Also – regulatory sequences, and other important structural elements
what are Eukaryotic chromosomes
-Linear molecules, held in the nucleus of the cell
-Often many chromosomes per genome
-Eg human genome = (typically) 22 pairs of chromosomes + 2 sex chromosomes, each between 5x107 and 2.5x109 bp
how do Centromeres help chromosomes segregate at mitosis and meiosis
-Centromere ( to help chromosomes separate and segregate ) = the specialised chromosomal region upon which the structures that link to spindle microtubules assemble and direct the equal segregation of chromosomes during mitosis and meiosis
-Doesn’t have to be in the centre of the chromosome!
-Variety of DNA sequences throughout the eukaryotes - but conserved histones
what are telomeres
-repetitive DNA at the ends of linear chromosomes
-protect chromosomes and stops ends being degraded as telomeres are the ends of the chromosomes
what are Prokaryotic genomes
-Bacteria generally (not always) have a single, circular chromosome
-Size typically a few million bp- smaller than human chromosomes
-Plasmids are also often found- also circular molecules
-Size typically a few thousand bp- can move through bacterial cells
-Can carry a variety of advantageous genes such as antibiotic resistance cassettes
-Passed between cells by conjugation (organised way of sharing a circular plasmid)
what are DNA-binding proteins
-DNA-binding domains in proteins
-General affinity for DNA (can more specific if needed)
-Or sequence-specific
-Can prefer single-stranded or double-stranded DNA
Roles of DNA-binding proteins:
-Regulate gene expression
-Cut DNA at specific sequences
-Protect DNA
Example 1 of DNA-binding proteins : transcriptional regulators
-Proteins that bind regulatory sequences near to the promoters of genes to either stimulate or block transcription. Bend the DNA into a favourable or unfavourable shape
-Example – the lac operon in E. coli – enzymes for breaking down lactose sugar
-Lac repressor binds to DNA and blocks transcription (when lactose is absent)
-Catabolic activator protein binds to DNA and increases transcription (when glucose is absent)
Example 2 of DNA-binding proteins: restriction endonucleases
-Enzymes that cut DNA at specific, normally palindromic, sequences 6-10 bp
-Originated in bacteria to RESTRICT the action of viruses
-Viral DNA is cut by the enzyme but bacterial DNA is methylated and therefore protected
-Used by scientists to manipulate DNA
Example 3 of DNA-binding proteins: histones
-Eukaryotic genomes are packaged into chromatin.
-DNA is wrapped around proteins called histones-Beads on a string structure
-Not sequence-specific
