ap bio unit 6

• DNA is located in the nucleoid region in prokaryotes and are smaller and often circular
• mRNA- messenger between DNA and the ribosomes

  rRNA- structural components of ribosomes

  tRNA- bring amino acids to ribosomes

  miRNA and siRNA- regulators of genes
• DNA replication is semiconservative, meaning that each strand in DNA acts as a template for the synthesis of a new, complementary strand

  
• helicase- unwinds the DNA at replication forks (breaking the hydrogen bonds between the nitrogenous base pairs)

  single-strand binding proteins- keep the separated strands from coming back together
• in E. coli, DNA polymerase III can only add nucleotides to the 3' end of an existing DNA strand (synthesizing the new strand in the 5 to 3 direction)

  • needs the enzyme called primase to make an RNA primer that is complementary to the template

  
• leading vs. lagging strand:

  • leading is synthesized TOWARDS the replication fork, while lagging is synthesized AWAY from the replication fork

  
• okazaki fragments- new DNA is made in these fragments on the lagging strand
• topoisomerase- prevents the DNA double helix ahead of the replication fork from getting too tightly wound as the DNA is opened up by helicase
• DNA polymerase I- RNA primers are removed and replaced by DNA

  • the spaces that remain after the primers are replaced get sealed by DNA ligase

  
• chargaff's rules- A = T and C = G
• eukaryotic RNA modifications after transcription:

  • protection- 5' cap and poly-A tail to protect the mRNA transcript from attack by enzymes in the cytoplasm called exonucleases
  • splicing- remove the introns (sequences of RNA that don't contain any information) from the mRNA transcript using spliceosomes
• transcription steps:

  1. initiation- RNA polymerase binds to the promoter of DNA (beginning of gene) and separates the DNA strands
  2. elongation- RNA polymerase reads DNA template strand and builds RNA strand of complementary nucleotides
  3. termination- terminator sequence signaling
• transcription- nucleus

  translation- ribosome
• alternative splicing- more than one mRNA can be made from the same gene

  
• translation:

  • initiation- ribosome assembles around mRNA, tRNA carrying MET matches AUG codon and is necessary to begin translation
  • elongation- amino acid chain gets longer
  • termination- stop codon enters ribosomes, triggering events that separate chain from tRNA
• coding strand = mRNA

  
• eukaryotes: transcription in nucleus, translation in ribosomes in cytosol

  prokaryotes: transcription AND translation in cytosol

  
• RNA in retroviruses
• lac operon (inducible)-

  • can be turned on by allolactose (inducer)
  • lac repressor originally blocks RNA polymerase from transcribing the lac operon when lactose is NOT AVAILABLE
  • when lactose IS AVAILABLE, allolactose (rearranged lactose) binds to the lac repressor, allowing it to change shape and not bind to the DNA
  • RNA polymerase can now transcribe the operon in order to BREAK DOWN LACTOSE

  
• the lac operon turns ON when glucose is UNAVAILABLE and lactose is AVAILABLE
• • the promoter region is the binding site for RNA polymerase
  • the operator region is the binding site for a repressor protein
• trp operon (repressible)-

  • can be turned off by tryptophan (corepressor) binding to the trp repressor
  • when tryptophan IS AVAILABLE, it is bound to the trp repressor and transcription is turned OFF
  • when tryptophan is NOT AVAILABLE, the trp repressor is NOT BOUND and RNA polymerase can make tryptophan

  
• tryptophan is present = trp repressor bound, trp operon NOT TRANSCRIBED

  tryptophan is NOT present = trp repressor unbound, trp operon is TRANSCRIBED to CREATE TRYPTOPHAN

  
• lac and trp operons are examples of gene regulation in BACTERIA
• eukaryotic gene regulation: growth factors

  • growth factor binds to receptor protein
  • triggers chemical events that activate transcription factors
  • transcription factors bind to DNA and cause transcription
• in prokaryotes, RNA polymerase attaches right to the DNA of the promoter, initiating transcription

  in eukaryotes, transcription factors help RNA polymerase attach to the promoter
• bacteria reproduce by splitting in two via binary fission

  • binary fission makes clones
• genetic variation in prokaryotes:

  • transformation- a bacterium takes up a piece of DNA floating in its environment

  
• genetic variation in prokaryotes:

  • transduction- DNA is accidentally moved from one bacterium to another by a virus
  • these viruses that infect bacteria are called bacteriophages
• genetic variation in prokaryotes:

  • conjugation- DNA is transferred from one bacterium to another through a pilus

  
• DNA cloning- process of making multiple identical copies of DNA

  • restriction enzyme: DNA-cutting enzyme that recognizes a specific target sequence and cuts DNA into two pieces at that site
  • joined together by DNA ligase

  
• bacterial transformation and selection in DNA cloning step 2-

  • plasmids and other DNA can be introduced into bacteria through transformation
  • during transformation, high temperature encourages the bacteria to take up foreign DNA
  • a plasmid typically contains an antibiotic resistance gene, which allows bacteria to survive in the presence of a specific antibiotic
  • bacteria without a plasmid will die, while bacteria carrying a plasmid can live and reproduce

  
• polymerase chain reaction (PCR): used to make many copies (millions) of a particular region of DNA

  1. denaturation: separate the DNA strands using heat
  2. annealing: primers can bind to their complementary sequences by cooling the reaction
  3. extension: raising the reaction temperatures for synthesis of new strands of DNA
• gel electrophoresis: used to separate DNA fragments based on their size and charge

  • DNA has a negative charge due to phosphate groups on backbone, so they start moving towards the positive pole
  • shorter DNA travel LONGER DISTANCES
• frederick griffith:

  • when the mice were exposed to an R strain (non-virulent) and a heat-killed S strain, they actually developed pneumonia and died
  • concluded that the R strain bacteria transformed and became a virulent strain
• mRNA modifications:

  • 5’ Guanine cap: signals the start of mRNA transcript for the ribosome to bind to; facilitates export from nucleus
  • Poly-A-tail: inhibits degradation of hydrolytic enzymes in cytosol
• Regulation of gene expression:

  • methylation- stop
  • acetylation- activate
• signal transduction pathways are highly specific and regulated

  • one molecule can cause a cascade effect of thousands of molecules
  • these pathways evolved from a COMMON ANCESTOR
• lac operon is INDUCIBLE, trp operon is REPRESSIBLE
• the same transcription factor often regulates different genes