double stranded DNA:
AGAGAGAGAGAGAGAGA TCTCTCTCTCTCTCTCTThe 2 hydrogen bonds of A pair exactly with the 2 H bonds of T The 3 hydrogen bonds of G pair exactly with the 3 H bonds of C
As the two strands split apart, two new strands are synthesized
"Template directed synthesis" Semi-conservative replication: Meselson-Stahl Experiment
Matthew Meselson has made many other discoveries, and was also chiefly responsible for persuading the US (via Kissinger) to abolish its germ warfare program in the early 1970s. Each single strand of DNA and RNA (unless they are circles) has a three-prime end and a five-prime end Ribose sugar is linked to phosphates at 3'carbon and 5'carbon. But new subunits can only be added at the 3' end! (for some reason) DNA synthesis enzymes are called DNA polymerase; The first such polymerases to be isolated (mid 1950s) later turned out to be for repair of damage, not regular copying. Then other polymerases were found, all of which added bases only at the 3-prime ends of the new chain. It was expected that the "real" DNA copying enzyme would be able to add to both strands simultaneously! But none exists! A MAJOR PARADOX!! This paradox was eventually solved by some strange discoveries
The true method is continuous elongation from 5' to 3' to form the "leading strand"
Topoisomerases are enzymes that allow coiled DNA strands to spin (by cutting one of the strands)
PCR = the Polymerase Chain Reaction Heating DNA, to nearly to boiling temperature (95 C.) causes the two strands to separate. Then cool, and add specific "primer" single-strand sequences.
Then add deoxyATP etc. and DNA polymerase enzyme
then heat again, to separate new strands. repeat cycle, repeat again When this method was first invented, you had to add more enzyme for each cycle, because the boiling destroyed it. But then certain bacteria from Yellowstone boiling springs were used as a source of heat resistant DNA polymerase.
PCR has been used to amplify mitochondrial DNA from bones of Neanderthal cave men
Sometimes in DNA copying, the wrong base gets added.
Ultraviolet light and many chemicals can damage DNA,
Special sets of enzymes find such damage, find "wrong" bases Without these special enzymes, mutation rates are much higher Some people have mutations in the genes for repair enzymes: "Xeroderma pigmentosa" causing their rates of skin cancer to be thousands of times higher.
Or, when the DNA is too badly damaged,
Most anti-cancer drugs damage DNA, often by cross-linking.
Nerve gas acts differently: by covalent bonding to -OH in serine
Iraq killed ~50,000+ Iranian soldiers with mustard gas
RNA copies are made by copying one strand of DNA; "Transcription" means making such RNA copies of DNA
Do not confuse the words transcription and translation; Please get used to them having the following meanings:
transcription = RNA synthesis
RNA synthesis is catalysed by enzymes called RNA polymerase Only certain special parts of DNA get copied (and only one of the two strands in any one region)
This is controlled by preferential binding of RNA polymerase to just certain base sequences pribnow box, etc. "promoter regions" To illustrate this fact: "Pseudogenes" are lengths of DNA where the base sequence codes for some actual protein, but has no promoter sequence upstream of the pseudogene. If you somehow inserted a promoter sequence upstream of a pseudogene, then an RNA for it would get transcribed. And what ought to happen if you inserted promoter sequences in random locations in an organism's genome? Three main categories of RNA (each coded for by its own genes = DNA sequences)
Transfer RNA: each binds to its own amino acid; so there are glycine t-RNAs, alanine t-RNAs etc. Ribosomal RNA (ribosomes are million+ molecular weight enzyme complexes where proteins are made from amino acids.)
Messenger RNA (that codes for the amino acid sequence of proteins, according to the genetic code) To everybody's great surprise, (most) eucaryote genes have introns, which are intercalated regions of many 10s or 100s of DNA base pairs that will NOT get translated, because these sequences will be cut out of the RNA transcripts! Nobody understands why they exist!
Procaryotes don't have introns. The genes for a few specific proteins (histones are an example) don't have introns. And some species have more and bigger introns in their genes that other species. Introns get copied into the m-RNA precursor, but then spliced out before the m-RNA goes to the cytoplasm.
The parts of the RNA that remain in the messenger are called "exons". For many proteins, several different versions get made, because of different processing of their m-RNA Other aspects of "processing" of messenger-RNA: "Caps" and "poly-A-tails: Questions that you should now be able to answer: 1) What are the raw materials from which DNA is synthesized?
2) If these raw materials were radioactively labeled, then after a double stranded DNA is copied to make two copies of this DNA, then where would the radioactive label be found? 3) What was confirmed by the famous "Meselson Stahl experiment? *4) Where would the radioactivity be after several more rounds of DNA strand duplication?
*5) In the preceding questions, we assumed that the radioactive label was in either the ribose, or in the purines and pyrimidines, 6) What are the names of the two different kinds of ends of DNA and RNA strands? *7) In double stranded DNA, the 3' end of one strand is next to what part of the other strand? 8) How can double stranded DNA uncoil and re-coil when being copied? *9) Are there any ways to inhibit this uncoiling in germs, but not animal cells? For what purpose might you want to do that? 10) When double stranded DNA is copied, are both strands copied the same way? Or what? 11) Does the wrong base ever get added in DNA synthesis? 12) Does the addition of the wrong base necessarily result in a mutation? What else might happen? 13) How can mutations in certain genes result in changing the rate of mutation of all genes, including themselves? 14) Where did the heat-resistant DNA polymerase come from? 15) For what specific method is this heat-resistant enzyme especially useful? 16) How is it possible to make large amounts of DNA, with the same base sequences, from tiny amounts of blood or other cells found at a crime scene? Could DNA be duplicated a billion-fold? *17) A few years ago, several students in Biology 52 turned out to believe that Darwinian evolution worked by having "bad" mutations edited out of the DNA, while "good" mutations were not edited out! What process had these students misunderstood? *18) To put the question another way: when enzymes selectively "fix" abnormal base sequences, can they do this based on the phenotype (= effect) of the mutation, or something else? 19*) Can this mechanism distinguish between mutations with good effects and mutations with bad effects? 20) How is repair of DNA damage related to one of the cell cycle checkpoints? 21) What are pseudogenes? What makes them different from genes? 22) Why wouldn't a mutation in a pseudogene have any effect on the phenotype of an organism? 23) Why would DNA repair mechanisms be just as likely to repair damage to DNA in pseudogenes as in actual genes? 24) How could mutations in the DNA near a pseudogene cause this gene to be transcribed into a messenger RNA? 25) What part of the gene for a transfer RNA would need to be mutated in order to cause it to bind to messenger RNA at the wrong codons? 26) How are introns related to the ability of some eucaryote genes to code for proteins of several different sizes, with slightly different properties? *27) Guess why ribosomes are (barely) visible as dots by transmission electron microscopy. 28) Besides splicing out the introns, what two other changes are made in "processing" eucaryote messenger RNA 29) In embryonic development, the control of gene expression is usually by "transcriptional control", but sometimes by "translational control". Figure out what these terms must mean.
If an egg contains stored messenger RNA, that doesn't get used to make protein until after fertilization, which type of control is that? 30) What's wrong with the statements, sometimes read in the newspaper, that DNA is converted into RNA and RNA is then converted into protein? What really happens? What is the misunderstanding?
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