chapter 3 Flashcards
what does the central dogma of molecular genetcis/fundamental dogma state?
- information flows from DNA to RNA to protein
what is the Hershey-Chase experiment?
- researchers used radiolabeled sulfur and phosphorous as a way of distinguishing between proteins (which contain S but not P naturally) and nucleic acids (which have P but not S) and used bacteriophages which inject genetic material into bacterial cells and concluded that the bacterial cells post-transduction contained radiolabeled P and not S indicating that the genetic material in question was DNA
the simplest version of the central dogma is?
- information is stored over the long term in DNA and is then transcribed into mRNA which are then translated into proteins
- note that reverse transcriptase allows DNA to be transcribed from RNA, reversing the normal flow of information
- several forms of non coding RNA exist including tRNA
what is the genetic code?
- DNA/RNS contain a genetic code
- each contain 4 bases whcih are combined to code for 20 amino acids
what are codons?
- combinations of 3 nucleobases code for amino acids
how many combinations of bases exist?
- 64 (43)
the genetic code has something called degeneracy meaning?
- A code in which several code words have the same meaning. The genetic code is degenerate because there are many instances in which different codons specify the same amino acid. A genetic code in which some amino acids may each be encoded by more than one codon.
What is the code for the start codon?
- AUG (methionine)
what are the 3 stop codons?
- UAG
- UGA
- UAA
codons for each amino acid usually have?
- the same first 2 amino acids but differ at the third (wobble) to provide some degree of protection against mutations
What are the basic points of the Watson-Crick model of DNA structure?
- DNA is organized in a double helix of antiparallel strands, with a sugar-phosphate backbone connected by phosphodiester bonds on the outside and nitrogenous bases on the inside
- complementary base-pairing dictates that A pairs with T and C pairs with G
- the interior of the structure is stabilized by hydrogen bonds between base pairs (2 for AT and 3 for GC) as well as hydrophobic interactions between stacked nitrogenous bases
in eukaroyes, DNA is organized into?
- linear chromosomes
Human cells normally have how many distinct chromosomes?
- 22 known as autosomes (somatic cells contain 2 copies of each of these chromosomes)
- 2 sex chromosomes (females 2x and male 1x1y)
- so in the standard human cell there are 46 chromosomes with 2 copies of each 22 autosomes and either of the 2 sex chromsomes
What are histones?
- proteins that act as spools for DNA to wind around
what are DNA-histone complexes called?
- nucleosomes that contain approximately 200 base pairs each
what is euchromatin?
- a loose configuration that is difficult to see under light microscopy and allows DNA to be readily transcribed
- throughout interphase, DNA generally exists as euchromatin which makes sense because this is the form that allows transcription to happen and for cellular activities to be carried out
what is heterochromatin?
- the tightly coiled, dense form of chromatin that is visible during cell division and is present to a lesser extent during interphase
what plays a major role int he interactions between histones and DNA?
- charge
what is the normal charge if histones?
- alkaline and positively charged at physiological pH which facilitates their interaction with the highly negatively charged phosphate groups on the backbone of DNA
how does acetylation affect histones?
- reduces their positive charge, making histones interact with DNA less closely, whcih in turn facilitates transcription activity
what is DNA replication
- the basis for genetic inheritance, because it is the process that allows DNA to be passed on to a daughter cell
- In replication, a DNA helix unwinds and a new complementary sequence is synthesized from each strand
- this process is known as semiconservative replication, because each new DNA sequence contains one strand from the original DNA molecule and one newly synthesized complement
what was the Meselson-Stahl experiment
Meselson and Stahl conducted their famous experiments on DNA replication using E. coli bacteria as a model system.
They began by growing E. coli in medium, or nutrient broth, containing a “heavy” isotope of nitrogen, 15N. When grown on medium containing heavy 15N, the bacteria took up the nitrogen and used it to synthesize new biological molecules, including DNA.
After many generations growing in the 15N, the nitrogenous bases of the bacteria’s DNA were all labeled with heavy 15N. Then, the bacteria were switched to medium containing a “light” 14N isotope and allowed to grow for several generations. DNA made after the switch would have to be made up of 14N, as this would have been the only nitrogen available for DNA synthesis.
Meselson and Stahl knew how often E. coli cells divided, so they were able to collect small samples in each generation and extract and purify the DNA. They then measured the density of the DNA (and, indirectly, its 15N and 14N) using density gradient centrifugation.
This method separates molecules such as DNA into bands by spinning them at high speeds in the presence of another molecule, such as cesium chloride, that forms a density gradient from the top to the bottom of the spinning tube. Density gradient centrifugation allows very small differences—like those between 15N and 14N end text-labeled DNA—to be detected.
Diagram of a test tube containing CsCl, nitrogen-14-labeled DNA, and nitrogen-15-labeled DNA following high-speed centrifugation. The density of the medium in the test tube is greatest at the bottom and least at the top, thanks to the formation of the CsCl gradient. The nitrogen-14-labeled DNA forms a band relatively close to the top of the test tube, while the nitrogen-15-labeled DNA forms a band closer to the bottom of the test tube. The positions of the bands reflect their relative densities.
Results of the experiment:
When DNA from the first four generations of E. coli was analyzed, it produced the pattern of semiconservative model
What did this result tell Meselson and Stahl? Let’s walk through the first few generations, which provide the key information.
Conclusion
The experiment done by Meselson and Stahl demonstrated that DNA replicated semi-conservatively, meaning that each strand in a DNA molecule serves as a template for synthesis of a new, complementary strand.
Although Meselson and Stahl did their experiments in the bacterium E. coli, we know today that semi-conservative DNA replication is a universal mechanism shared by all organisms on planet Earth. Some of your cells are replicating their DNA semi-conservatively right now!
Where does DNA replication begin?
- the origin of replication whcih has specific sequences that binds with a protein complex known as the pre-replication complex and tend to have high AT content
- bacterial genomes have one origin of replication from which replication proceeds bidirectionally
- eukaryotic chromosomes have multiple origins of replication and the centromeme connects the sister chromatids that are created during this process
what does DNA helicase do in DNA replication?
- unwinds the DNA helix and separates the two strands of DNA
what does single-stranded DNA binding proteinds do in DNA replication?
- keep the separated strands from immediately re-annealing
what does primase do in DNA replication?
- synthesizes a short RNA primer with free 3’ OH group that is used as the starting point for the synthesis of a new strand
what does DNA polymerase do in DNA replication?
- reads the DNA in a 3’ to 5’ direction and synthesizes the complementary strand in the 5’ to 3’ direction
what does DNA gyrase do in DNA replication?
- AKA DNA topoisomerase II
- alleviates the supercoiling that would otherwise be created as helicase works its way down the DNA molecule
In transcription, the template strand is known as?
- the antisense strand and the opposite strand is known as the sense strand becuase it corresponds to the codons on the mRNA that is eventually exported to the cytosol for translation
what is splicing?
- in splicing, noncoding sequences (introns) are removed and coding sequences (exons) are ligated together
- exons can be ligated in different combinations to increase the amount of different, but related proteins that can be expressed from a single gene
- explains why there are over 200,000 proteins in the human body, but only approximately 20,000 genes
- splicing is carried out by the spliceosome, a combination of small nuclear RNAs (snRNA) and protein complexes (when combined, they are known as small nuclear ribonuclear proteins (snRNPs)
What are the 3 binding sites that are involved in elongation?
- the A site- contains the next aminoacyl-tRNA complex
- P site- a peptide bond is formed between the growing polypeptide chain and the incoming amino acid
- E site- the tRNA which is now no longer “charged”, briefly pauses at this site and detaches from the mRNA. this process continues until termination, when a stop codon (UGA, UAG, UAA) on the mRNA is encountered, at which point a release factor triggers ribosome disassembly and release the polypeptide
