history of DNA research/discovery

in the early 1800s, scientists thought protein was the hereditary material

• proteins are variable in structure, DNA is too repetitive

• griffith finds a "transforming principle"

• concluded that the material transferred over from the heat killed S bacteria to the live R bacteria

• whatever it was changed the harmless R bacteria into disease-causing S bacteria

• he called the mystery the "transforming principle"

• alfred hershey + martha chase

• provided evidence that DNA is the genetic material

• studied viruses that infect bacteria — "bacteriophage" or "phage"

• proteins contain sulfur, but little phosphorus, and DNA contains phosphorus but no sulfur

• grew phages in cultures with radioactive phosphorus and sulfur and had them infect bacteria

• conclusion: the protein coat was left outside and the DNA entered. DNA is hereditary material!

structure of DNA

• DNA is a long polymer of repeating units called nucleotides

• nucleotides are the monomers/building blocks of DNA

• nucleotides consist of

• a deoxyribose sugar

• a nitrogenous base

• a phosphate group

• there are four different bases - adenine, guanine, cytosine, thymine

• cytosine and thymine have a single ring structure and are called pyrimidines

• adenine and guanine have a double ring structure and are called purines

• erwin chargaff: found that the same 4 bases are found in all organisms. He noticed that in each organism, adenine and thymine were found in equal amounts as well as cytosine and guanine.

• watson and crick: found DNA to be a double helix "twisted ladder"

• used information from rosalind franklin, maurice wilkins + chargaff

DNA replication

• semiconservative

• each new strand conserves part of the original

• parent ("template") strands → new strands

• The largest chromosome has 250 million nucleotides and a diploid cell contains around 6 billion base pairs. that's going to take some time to replicate! It takes 8 hours to complete S of interphase.

• The first thing that happens is the unwinding of the DNA molecule. this is done by enzyme helicase

• while the DNA is unwinding, single strand binding proteins (SSBs) stabilize + prevent it from retwisting while the new nucleotides are added

• Many origins of replications allow it to go faster than just starting on one end. each starting spot forms a replication bubble

• while the DNA is being unwound, a team of enzymes go to work replicating both sides of the molecule

• DNA polymerase III: responsible for adding new nucleotides

• How does DNA polymerase III know where to begin? think of an airplane pilot — how do they know where to land the plane?

• there has to be a signal telling DNA polymerase III where to attach and begin building the new strands. Just like a runway has lights at night for the pilot to land, there is an enzyme called primase that lays down the signal.

• the signal is an RNA primer: a short sequence of RNA nucleotides

• DNA strands are antiparallel — one side is basically upside down and the sugar points in the opposite direction

• the sugar molecule is shaped like a pentagon and acts like it has a trailer hitch in the back; just like your vehicle can only attach and pull things from the back end, so can the sugar

• the sugar molecule like a car; pointing in the direction it's traveling and the flat end has the trailer hitch; the front has the 5' carbon and the back has the 3' carbon

• Why is this important?

• DNA polymerase can only add new nucleotides onto the 3' end of the growing strand. because the two sides are antiparallel (upside down), the two new strands get their nucleotides added in different ways

• when we build two new DNA strands, the leading strand is assembled continuously in a 5' to 3' direction

• remember we can only add new nucleotides on the 3' carbon end of the sugar — think trailer hitch

• The other strand (the lagging strand) has to be built discontinuously because we can't add new nucleotides to the front.

• it would be like attaching the camper to the front of the car instead of the trailer hitch in the back of it

• so, RNA primers are put down in front and polymerase adds the nucleotides on the 3' end of the sugar working backwards

enzymes involved in replication

• DNA polymerase III: an enzyme that adds the new nucleotides to the growing stand, and proofreads for mistakes

• DNA ligase: enzyme that links/glues the okazaki fragments together

• primase: an enzyme that puts down the RNA primer

• RNA primer: a short segment of RNA that signals DNA polymerase where to begin replication

• okazaki fragments: the new nucleotide fragments added on the lagging strand

differences between DNA and RNA

• DNA: double stranded - sugar is deoxyribose - bases are AGCT

• RNA: single stranded - sugar is ribose - bases are AGCU

DNA transcription + translation

• transcription: the making of an mRNA molecule from a DNA template

• starts with RNA polymerase recognizing a promoter region (TATA box) just upstream of the gene to be copied

• RNA polymerase adds RNA nucleotides complementary to DNA until it reaches a terminator sequence

• triplet codon: a sequence of three bases that code for an amino acid

• codon: a specific sequence of three consecutive nucleotides that is part of the genetic code and that specifies a particular amino acid or starts / stops protein synthesis

• gene: a sequence of nucleotides on the DNA molecule that codes for the production of a particular protein

• translation: tRNA molecules read the triplet codons by their own 3-letter anticodons

• each tRNA is specific and can only bring in one amino acid

• methionine: always the first amino acid - AUG is the triplet codon on mRNA (TAC og)

• translation continues until a STOP codon is read from the mRNA

• 600 amino acids are added per minute

• ribosome structure: A-site, P-site, E-site

• A site: holds incoming tRNA and amino acids

• P site: tRNA holds the growing protein

• E site: tRNA exits

types of RNA

• rRNA: structural RNA - ribosomes are made of this

• mRNA: messenger RNA - made in transcription - leaves the nucleus to deliver instructions to the ribosome

• tRNA: transfer RNA - located at the ribosome - translate the mRNA and ring in the correct amino acids

gene regulation and expression in prokaryotes

• it allows bacteria to conserve energy

• promoter: a DNA segment that helps RNA polymerase know where to start transcription

• operator: a DNA segment that turns a gene on or off

• operon: a region of DNA that includes the promoter and operator and the genes to be transcribed into protein

mutations

• mutation: any change in the genetic information of a cell

• mutagen: a physical or chemical agent that can increase the likelihood of a mutation

• point mutations: nucleotide substitutions — the replacement of one nucleotide and its base-pairing partner with another pair of nucleotides

• point mutations can result in

• a silent mutation: the mRNA codon might be different but it still codes for the same amino acid, so the resulting protein isn't affected, GAA to GAG (both code for the AA - GLU)

• a missense mutation: in this case the wrong amino acid is coded. this can have no effect or cause the protein to not perform its normal function (sickle cell disease)

• a nonsense mutation: the amino acid is changed to a stop codon and the result is a prematurely terminated protein

• a frameshift mutation: when a nucleotide is either inserted or deleted, it regroups the codons and disrupts the reading frame. Usually, a non-functional protein is built and has negative effects.

1. anagram: THE CAT ATE THE RAT — if we delete the letter E, the reading frame gets shifted over: THC ATA TET HER AT — this will cause the wrong amino acid and therefore an incorrect protein to be built

• chromosome mutations * refer to diagrams on notes

• duplication, translocation