| What were the candidates for genetic material? | When T. H. Morgan’s group showed that genes are located on chromosomes, the two components of chromosomes—DNA and protein—became candidates for the genetic material |
| How did they find that DNA was genetic material? Transformation? | - by studying bacteria and the viruses that infect them
- Frederick Griffith (worked with two strains of a bacterium, one pathogenic [cause disease] and one harmless)
- mixed killed remains of pathogenic strain with living cells of harmless strain
- some living cells ended up becoming pathogenic
- He called this phenomenon transformation (now defined as a change in genotype and phenotype due to assimilation of foreign DNA)
- work by later scientists identified the transforming substance as DNA (some biologists were skeptical though bc there wasn't a lot of info on DNA) |
| Why did the cells in Frederick Griffith's experiment act the way they did? | Bacteria DNA can uptake another bacteria cell's DNA. Meaning, a bacteria cell can incorporate another bacteria DNA into their DNA. That's why the harmless bacteria became disease bacteria. |
| bacteriophages (or phages)? | - More evidence for DNA as the genetic material came from studies of viruses that infect bacteria
- Such viruses are called bacteriophages (or phages)
- Phages have been widely used as tools by researchers in molecular genetics |
| Virus? Capsid? | - A virus is DNA (sometimes RNA) enclosed by a protective coat (Capsid: the protective coat that protects DNA in virus)
- Virus injects its DNA into host cell
- Then, many of its babies burst out of the infected cell |
| Experiment that showed that DNA is the genetic material of a phage | - Alfred Hershey and Martha Chase showed that DNA is the genetic material of a phage known as T2
- They designed an experiment showing that only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection
- They concluded that the injected DNA of the phage provides the genetic information |
| DNA | - DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group
- The nitrogenous bases can be adenine (A), thymine (T), guanine (G), or cytosine (C)
- Sugar shape: Pentagon
- Sugar: Deoxyribose
- Shape of Nitrogenous base: Hexagon
- Phosphate group shape: Circle
- Locations: Nitrogen bases are rungs of ladder, sugar and phosphate are the outer portions of the ladder
(^^ reference pic ^^)
- Hydrogen bonds hold nitrogenous bases together (like when they pair up) |
| Chargaff’s rules | - Erwin Chargaff reported that DNA composition varies from one species to the next
- This evidence of molecular diversity among organisms made DNA a more credible candidate for the genetic material
- Two findings became known as Chargaff’s rules:
- The base composition of DNA varies between species
- In any species the number of A and T bases is equal and the number of G and C bases is equal |
| Structural Model of DNA | - Maurice Wilkins and Rosalind Franklin used a technique called X-ray crystallography to study molecular structure
- Franklin produced a picture of the DNA molecule using this technique
- Franklin’s X-ray crystallographic images of DNA allowed James Watson to deduce that DNA was helical and what the width of the helix and the spacing of the nitrogenous bases were
- The pattern in the photo suggested that the DNA molecule was made up of two strands, forming a double helix
- Watson built a model in which the sugar-phosphate backbones were antiparallel (their subunits run in opposite directions) |
| How did Watson and Crick figure out the nitrogenous bases pairing | - At first, Watson and Crick thought the bases paired like with like (A with A, and so on), but such pairings did not result in a uniform width
- Instead, pairing a purine (A or G) with a pyrimidine (C or T) resulted in a uniform width consistent with the X-ray data
- They determined that adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C) |
| Differences between DNA and RNA | - DNA has two strands, while RNA has one
- DNA sugar is deoxyribose, RNA sugar is ribose
- Uracil is in RNA (takes place of thymine)
- DNA and RNA have the same shapes for things like sugars tho |
| DNA Replication | - The copying of DNA
- Resemblance of offspring to parents relies on accurate replication of DNA prior to meiosis and its transmission to the next generation
- Replication prior to mitosis ensures the faithful transmission of genetic information from a parent cell to the two daughter cells
- Since the two strands of DNA are complementary [MEANING THEY FOLLOW THE SAME PAIRING RULES], each strand acts as a template for building a new strand in replication
- This yields two exact replicas of the “parental” molecule |
| Semiconservative model | - Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand
- Competing models were the conservative model (the two parent strands rejoin) and the dispersive model (each strand is a mix of old and new)
- The Semiconservative Model ended up being correct |
| Origins of replication | - Replication begins at particular sites called origins of replication
- At these sites, two DNA strands are separated, opening up a replication “bubble”
- A eukaryotic chromosome may have a lottttt of these origins of replication
- Replication proceeds in both directions from each origin, until the entire molecule is copied
[see image - note: the shape of DNA in bacteria cells is circular] |
| Replication fork | - At the end of each replication bubble is a replication fork, a Y-shaped region where parental DNA strands are being unwound
- There are two (one at each end), this is where the DNA gets opened up |
| Helicases | Helicases are enzymes that untwist the double helix at the replication forks |
| Single-strand binding proteins | Single-strand binding proteins bind to and stabilize single-stranded DNA
[PROBABLY DON'T NEED TO KNOW THIS] |
| Topoisomerase | Topoisomerase relieves the strain of twisting of the double helix by breaking, swiveling, and rejoining DNA strands |
| Primer | - DNA polymerases require a primer to which they can add nucleotides
- The initial nucleotide chain is a short R N A primer
- The completed primer is small
- The new D N A strand will start from the 3′ end of the R N A primer |
| Primase | - an enzyme that synthesizes the RNA primer
- "Primase is like dropping a signal, telling where replication will occur" |
| Orientation of strands | - the strands go from 5' - 3' OR 3' - 5'
- See IMAGE !! Note the direction of the RNA Primer (shown to be <- 3' - 5')
- extra note for fun: the 5' end has a free phosphate on a 5' carbon and the 3' end has a free phosphate on a 3' carbon (Remember how the carbon atoms in the sugar ring are number 1' to 5', like we learned in chemistry) |
| DNA polymerases | - Enzymes called DNA polymerases catalyze the synthesis of new DNA at a replication fork
- Most DNA polymerases require a primer and a DNA template strand
- Reads strands, makes new DNA strand |
| Antiparallel Elongation | - The antiparallel structure of the double helix affects replication
- DNA polymerases add nucleotides only to the free 3′ end of a growing strand; therefore, a new DNA strand can elongate only in the 5′ → 3′ direction |
| Leading strand | - Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork
- Building and moving in opposite directions (see image to see the directions things are going in) |
| Lagging strand? Okazaki fragments? DNA Ligase? | - To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork
- The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase
[see image] |
| Enzymes and Functions | - DNA polymerase: builds DNA, matches pairs, adds nucleotides to RNA primer or pre-existing DNA strands, can remove RNA nucleotides of primer and replace them w/ DNA nucleotides (see table image)
- Topoisomerase: Release tensions
- Helicase: Untwists
- Primase: Makes primer, helps polymerase attach
- Ligase: Joins Okazaki fragments of lagging strand (see table image) |
| The DNA Replication Complex | [not tooo important]
- The proteins that participate in DNA replication form a large complex, a “DNA replication machine”
- The DNA replication machine may be stationary during the replication process
- Recent studies support a model in which DNA polymerase molecules “reel in” parental DNA and extrude newly made daughter DNA molecules
- The exact mechanism is not yet resolved |
| mismatch repair of DNA | - DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides
- In mismatch repair of DNA, repair enzymes replace incorrectly paired nucleotides that have evaded the proofreading process |
| Mutations | - The error rate after proofreading and repair is low but not zero
- Sequence changes may become permanent and can be passed on to the next generation
- These changes (mutations) are the source of the genetic variation upon which natural selection operates and are ultimately responsible for the appearance of new species |
| What happens to DNA when your get old | As you get old, your DNA can be too small or uneven (repeated rounds of replication produce shorter DNA molecules with uneven ends), and gradually get damaged at the ends (telomere: ends of chromosomes). This plays a role in why children of older parents are more likely to have disabilities. |
| telomeres | - Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends called telomeres
- Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules
- It has been proposed that the shortening of telomeres is connected to aging |
| telomerase | - If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce
- An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells
- The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions
- There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist |
| DNA in bacteria vs Eukaryotes? Chromatin? | - The bacterial chromosome is a double-stranded, circular DNA molecule associated with a small amount of protein. In a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid- Eukaryotic chromosomes have linear DNA molecules associated with a large amountof protein. In the eukaryotic cell, DNA is precisely combined with proteins in a complex called chromatin. Chromatin is loosely packed in nucleus during interphase and condenses prior to mitosis. If DNA is more packed, it is harder to read DNA and use instructions. Chromatin undergoes changes in packing during the cell cycle |
| histones | - Proteins called histones are responsible for the main level of DNA packing in interphase chromatin (help in condensing chromatin ~~)
- Histones can undergo chemical modifications that result in changes in chromatin condensation
- These changes can also have multiple effects on gene expression |
