DNA, RNA, and the Flow of Genetic Information

Nucleic Acid Structure What structural features do DNA and RNA share? What structural features do DNA and RNA share?  Polymers of nucleotides  Each nucleotide contains sugar, phosphate, nitrogen containing base  Each nucleic acid contains 4 different nucleotides

Nucleic Acid Structure What differentiates DNA from RNA? What differentiates DNA from RNA?  Type of pentose sugar

Nucleic Acid Structure  The nitrogen containing bases derived from purine and pyrimidine

Nucleic Acid Structure What makes up the backbone of the nucleic acids? What makes up the backbone of the nucleic acids?

Nucleic Acid Structure What contributes to the stability of nucleic acids? What contributes to the stability of nucleic acids?  Negative charge of phosphodiester bridge  Repels nucleophiles What is the difference between a nucleotide and a nucleoside? What is the difference between a nucleotide and a nucleoside?

Nucleic Acid Structure What are the DNA nucleotides? What are the DNA nucleotides?  Deoxyadenosine-5-phosphate  Deoxyguanosine-5-phosphate  Deoxycytidine-5-phosphote  Deoxythymidine-5-phosphate

Nucleic Acid Structure What are the RNA nucleotides? What are the RNA nucleotides?  Adenosine-5-phosphate  Guanosine-5-phosphate  Cytidine-5-phosphate  Uridine-5-phosphate

Nucleic Acid Structure How is the base bound to a sugar? How is the base bound to a sugar?   -glycosidic linkage

Nucleic Acid Structure Nucleic acids show polarity and are always written in the 5’ to 3’ direction Nucleic acids show polarity and are always written in the 5’ to 3’ direction

What doe this photograph represent? What doe this photograph represent? Nucleic Acid Structure

What are the major features of the double helix of DNA? What are the major features of the double helix of DNA?  Two chains coiled around common axis running in opposite directions  Bases on inside, sugar-phosphate on outside  Bases are 3.4Å apart  Structure repeats ever 34Å  Diameter = 20Å

Nucleic Acid Structure  Base pairing exists  A with T  C with G  How did the work of Chargaff support this concept?

DNA Replication DNA is said to replicate semiconservatively. What does this mean? DNA is said to replicate semiconservatively. What does this mean? How did Meselson and Stahl demonstrate this to be true? How did Meselson and Stahl demonstrate this to be true?

DNA How can the helical structure be disrupted? How can the helical structure be disrupted?  Heating What is T m ? What is T m ?  Melting temperature – half helical structure is destroyed What is hyperchromism? What is hyperchromism?  Single stranded DNA absorbs UV light more effectively than double stranded DNA

DNA

Why is the ability to separate the two chains of the double helix and reassociate them an important tool in the laboratory? Why is the ability to separate the two chains of the double helix and reassociate them an important tool in the laboratory?  hybridization experiments

DNA What is the difference between linear DNA and circular DNA and where are each of these forms found? What is the difference between linear DNA and circular DNA and where are each of these forms found?  circular – ends of molecule are linked  linear – human DNA  circular – bacterial DNA

DNA What is supercoiled DNA? What is supercoiled DNA?

Nucleic Acid Structures What are stem-loop structures? What are stem-loop structures?

Nucleic Acid Structures Other complex structures of single- stranded nucleic acids form Other complex structures of single- stranded nucleic acids form

Nucleic Acid Structures In some complex structures can get hydrogen bonds formed between non- standard base pairs In some complex structures can get hydrogen bonds formed between non- standard base pairs

Nucleic Acid Structures

DNA Replication What is DNA polymerase? What is DNA polymerase?  enzyme that catalyzes addition of DNA nucleotides to a growing chain of DNA  (DNA) n + dNTP (DNA) n+1 + PP i What besides the enzyme is needed for DNA synthesis? What besides the enzyme is needed for DNA synthesis?  template  primer  activated nucleotides

DNA Replication What is the nature of the reaction catalyzed by DNA polymerase? What is the nature of the reaction catalyzed by DNA polymerase?

DNA Replication What else can some DNA polymerases do? What else can some DNA polymerases do?  remove mismatched nucleotides

RNA Viruses What is the difference between and RNA virus and a retrovirus? What is the difference between and RNA virus and a retrovirus?  RNA viruses replicate via an RNA directed RNA polymerase  retroviruses use reverse transcriptase to replicate Examples of each? Examples of each?

Replication of Retrovirus

Gene Expression How does RNA facilitate gene expression? How does RNA facilitate gene expression?  m-RNA – carries information from DNA  t-RNA – carries amino acids to site of protein synthesis  r-RNA – major component of ribosome where proteins are made  snRNA – (in eucaryotes only) – splices RNA

Transcription What does RNA polymerase do and how does it work? What does RNA polymerase do and how does it work?

Transcription How does RNA polymerase differ from DNA polymerase? How does RNA polymerase differ from DNA polymerase?  doesn’t require primer  doesn’t contain nuclease activity

Transcription What are promoter sites and where are they located? What are promoter sites and where are they located?  regions of DNA that bind RNA polymerase and determine where transcription begins

Transcription How does RNA polymerase know when to stop transcribing? How does RNA polymerase know when to stop transcribing?  terminator sequence  rho protein

Transcription What happens to m-RNA in eukaryotes after transcription? What happens to m-RNA in eukaryotes after transcription?

Transcription How does t-RNA serve as an adaptor molecule? How does t-RNA serve as an adaptor molecule?

Transcription What do we know about the genetic code? What do we know about the genetic code?  three nucleotides code for an amino acid  code doesn’t overlap  no punctuation  code is degenerate

Genetic Code

Translation What are the start and stop signals for translation? What are the start and stop signals for translation?  stop codons – UAA, UCA,UAG

Genetic Code What evidence suggests that the genetic code is universal? What evidence suggests that the genetic code is universal?  one can use machinery of one species to translate m-RNA of a different species There are some variations in genetic code There are some variations in genetic code  mitocondrial DNA  DNA from cilliates

Genetic Code What are introns and exons? What are introns and exons?  introns – non-coding sequences of DNA  exons – coding sequences of DNA

RNA Processing How are introns correctly removed before translation? How are introns correctly removed before translation?  splicosomes – proteins and small RNA molecules

Exons and Introns Why are many genes in higher eukaryotes discontinuous? Why are many genes in higher eukaryotes discontinuous?  exons code functional domains in proteins  can shuffle exons to produce new proteins  can generate related proteins by splicing m-RNA differently