AP Biology : 4.3 Signal Transduction – Study Notes

C. DNA Replication
➢ First step is to unwind the double helix by breaking the hydrogen bonds

  •  Accomplished by an enzyme helicase
  • Single stranded Binding Protein hold the strands apart
  •  Origin of replication=place where replication process begins; short stretch of DNA with specific nucleotide sequence
  •  Exposed DNA now forms a y-shaped replication fork

➢ DNA replication begins at specific sites called origins of replication

Topoisomerase cuts and rejoins the helix to prevent tangling and relieve tension

DNA polymerase III adds nucleotides to freshly built strand

  •  Can only add nucleotides to the 3’ end

RNA primase adds a short strand of RNA nucleotides called an RNA primer


  •  Primase synthesizes RNA primer
  •  After replication, the DNA Polymerase I removes the RNA primer and replaces it with DNA

➢ Leading strand

  •  Synthesized continuously
  •  $5’ to 3’$
  •  Replicated towards fork

➢ Lagging strand

  •  Made in pieces called Okazaki fragments
  •  $3’ to 5’$
  •  Replicated Away from fork
  • Must be made in pieces since nucleotides can only added to 3’ end
  • Fragments linked together by DNA ligase to produce a continuous strand

➢ DNA proofreading and repair

  • DNA polymerase in charge of repair synthesis
  •  Nuclease removes damage
  •  Ligase seals newly repaired strands
  •  Repair enzymes detect damage

➢ Replicates semiconservatively because each new molecule is comprised of ½ of the original strand

  • Semiconservative model proved by Meselson and Stahl’s experiments
    ■ Created “heavy” template DNA using N15, measured weights of replicated DNA by looking at the layers that formed, semiconservative model was the only one that fit

➢ A few bases at very end cannot be replicated because the DNA polymerase needs to bind

  •  Every time replication occurs the chromosome loses a few base pairs
  •  Genome has compensated for this over time by putting bits of unimportant/less important DNA at the ends of a molecules called telomere

➢ Key history

  •  Protein originally thought to be the carrier of genetic material due to its higher variety and specific functions
  •  Griffiths want to find out what substance causes transformation

R bacteria had been transformed into pathogenic S bacteria by unknown substance

  •  A very, MacLeod, and McCarty isolated various cellular components from a dead virulent strain of bacteria
    ■ Followed up on a previous experiment by Griffiths and added each of these cellular components to a strain of living nonvirulent bacteria
    ■ Only the component of the deadly bacteria was able to change the second bacteria into a deadly strain capable of reproducing
    ■ DNA must be responsible for passing traits and it is inheritable


  • Hershey-CHase

■ Used bacteriophages and labelled protein parts of some with radiolabeled sulfur and labelled the DNA parts of other viruses with radiolabeled phosphorus

■ Bacteriophages inject genetic material into cell so more genetic material will be created

■ When viruses infected bacteria, only the labelled DNA was inside, but they were still able to replicate and make progeny viruses

■ E. coli were infected by the phage, and there was more and more P that entered. They concluded that DNA carried the genetic information to produce DNA and proteins

➢ Central Dogma

  •  DNA’s main role is directing the manufacture of molecules that actually do the work in the body
  •  DNA expression:
  •  1. Turn into RNA
  •  2. Send RNA out into the cell and often gets turned into a protein

Transcription turns RNA into DNA

  • Takes place in nucleus (except in prokaryotes)

➢ Translation turns RNA into a protein

  •  Takes place in cytoplasm


  • Single stranded
  •  5-carbon sugar is ribose instead of deoxyribose
  •  Uses uracil instead of thymine
  •  major types of RNA
    Messenger RNA (mRNA)
                  ● Temporary version of DNA that gets sent to ribosome
    Ribosomal RNA (rRNA)
                    ● Produced in nucleolus
                    ● Makes up part of ribosomes
    ■ Transfer RNA (tRNA)
                    ● Shuttles Amino acids to the ribosomes
                    ● Responsible for bringing the appropriate amino acids into place at the appropriate time
                    ● Done by reading message carried by mRNA
    Interfering RNA (RNAi)
                    ● Small snippets of RNA that are naturally made in the body or intentionally created by humans
                   ● siRNA and miRNA can bind to specific sequences of RNA and mark them for destruction

➢ Transcription

  •  RNA copy of DNA code
    ■ pre-mRNA synthesis
  • Only a specific section is copied into mRNA
  •  Occurs as-needed on a gene-by-gene basis
  • Exception: prokaryotes will transcribe a recipe that can be used to make several proteins
    ■ Called polycistronic transcript

             ■ Eukaryotes tend to have one gene that gets transcribed to one mRNA and translated into one protein
Monocistronic transcript

  •  3 steps: initiation, elongation, termination
    ■ initiation
                ● Unwind and unzip DNA strands using helicase
                ● Transcription initiation complex
  •  Transcription factor proteins+RNA polymerase
  • Forms at promoter
               ● Transcription only occurs as-needed to conserve resources
    ■ ELongation
                ● Begins at special sequences of the DNA strand called promoters
                 ● Free RNA nucleotides inside the nucleus used to create mRNA
  •  RNA polymerase used to construct mRNA
                 ● Strand that serves as the template is called antisense strand, the noncoding strand, or the template strand
                ● Strand that lies dormant is the sense strand, or the coding strand
                ● Rna polymerase build RNA only to 3’ side
  •  Doesn’t need primer
                  ● Promoter region is “upstream” of the actual coding part of the gene
                  ● Official starting point if start site
                 ● RNA strand is complementary to template DNA strand
    ■ Termination
              ● Once termination sequence is reached, it separates from the DNA template, completing the process of transcription

➢ RNA processing

  •  In eukaryotes the RNA must be processed before it can leave the nucleus
  • Freshly transcribed RNA is called hnRNA (heterogenous nuclear RNA) and it contains both coding regions and noncoding regions
  • Regions that express the code will be turned into protein are exons
  •  Non-coding regions in the mRNA are introns
    ■ Introns removed by spliceosome
           ● Spliceosome made up of many snRNPs
  •  snRNPs made up of ribozyme+small nuclear RNA
    ■ ribozyme=RNA catalyst that can copy RNA strands
             ● Spliceosome identifies ends of an intron
             ● Folds chromosome
            ● Spliceosome cuts out the intron and binds the two exons together
            ● Non i prokaryotic cells

● 3 properties of RNA that allow it to function as an enzyme

  •  Single stranded
  •  Functional groups that act as catalysts
  • Hydrogen bonds with other nucleic acids
      ■ Introns allow more genetic diversity
                  ● More possibilities for crossover
                  ● Alternate splicing can yield new protein varieties
  •  Methyl cap added to 5’ end
     ■ Helps mRNA leave nucleus
     ■ Allows attachment to ribosome
     ■ Modified guanine

○ poly-A tail added to 3’ end
             ■ Protects mRNA from endonucleases in cytoplasm, which can only attach to 3’ end
             ■ 50-250 adenine
○ No cap or tail in prokaryotic cells since they have no nucleus
○ mRNA leaves nucleus through nuclear pore

➢ TRanslation

  • Process of turning mRNA into a protein
  •  mRNA nucleotides will be read in the ribosome in groups of three
    ■ Group of three nucleotides=codon
    ● Each codon corresponds to a particular amino acid
  •  mRNA attaches to the ribosomes to initiate translation and “waits” for the amino acids to come to the ribosome
  • 3 sites on ribosome
    ■ E=exit site
    ■ P=polypeptide storage/exit
    ■ A= place where tRNA brings in amino acid
  •  1.mRNA attaches to mRNA binding site on small subunit. tRNA attaches onto A site
  •  2. Large subunit attaches via GTP
    ■ 1st tRNA is in P site
    ■ 2nd tRNA comes in A site
  •  3. rRNA in large subunit catalyzes a peptide bond between amino acids

○ 4. 1st rRNA moves to exit site
■ 2nd tRNA moves to P site
■ New tRNA comes in through A site
■ Steps 1-4 repeats until stop codon is reached
■ As mRNA moves through ribosome, other ribosomes can attach to it at the same time (as long as mRNA has not degraded, especially on 5’cap

  • 5. Release factor adds water to end of polypeptide; polypeptide detaches and exits
    through P-site tunnel
  • 6. small/large subunit/mRNA disassemble and disassociate; process of translation can start over again
  •  tRNA carries amino acid
    ■ Attaches to RNA via anticodon (complementary base pair to codon)
    Wobble pairing on third nucleotide (flexible bonds)
    ■ Each tRNA becomes charged and enzymatically attaches to an amino acid in the cell’s cytoplasm and “shuttle” it to the ribosome
    ■ Charging enzymes require ATP
  •  3 phases:
    ■ Initiation
    ● 3 binding sites:
  •  A site
  •  P site
  • E site
    ● Start codon is AUG (methionine)
    ● TATA box=specific promoter for initiation
    ● RNA polymerase binds to a specific location on promoter
    ● Transcription factors attach to promoter to help guide RNA polymerase
    ■ Elongation
    ● As each amino acid is brought to the mRNA, it is linked to its neighboring amino acid by a peptide bond and eventually forms a full protein
    ■ Termination
    ● Synthesis of a polypeptide ended by stop codons

➢ Gene Regulation

  •  Pre-transcriptional regulation
    ■ Transcription factors can either encourage or inhibit the unwinding of DNA and the binding of RNA polymerase
  • Operons
    ■ Bacteria only
    ■ Structural genes
    ● Code for enzymes in a chemical reaction
    ● Genes will be transcribed at the same time to produce particular enzymes
    ■ Promoter gene
    ● Region where RNA polymerase binds to begin transcription
    ■ Operator
    ● Controls whether transcription will occur
    ● Where repressor/inducer binds
    ■ Regulatory gene
    ● Codes for a specific regulatory protein called to repressor
    ● Repressor capable of attaching to the operator and blocking transcription
    ● If repressor binds to the operator, transcription will not occur
    ● If repressor does not bind to the operator, RNA moves along operator and transcription occurs
    ■ inducible=presence of molecule turns gene on
    ■ repressible=presence of molecule turns gene off


  • Chromatin Modification
    ■ Histone acetylation
                ● Acetyl groups added to histones
                ● Looser Chromatin
                ● Access for transcription increased
    ■ DNA methylation
               ● Methyl groups added to bases
              ● Silences gene
              ● Tightens chromatin
  •  Enhancers

  • Post-transcriptional regulation
    ■ Occurs when the cell creates an RNA but then decides that it should not be translated into a protein
    ■ RNAi molecules bind to an RNA via complementary base pairing
    ■ Creates double-stranded RNA, signalling that RNA should be destroyed, preventing it from being translated
  •  Post-translational regulation
    ■ Protein has already been made, but doesn’t need it yet, so it is deactivated

➢ Mutations

  •  Mutation is an error in the genetic code
  •  Occur because DNA is damaged in cannot be repaired or because DNA is repaired incorrectly
    ■ Caused by chemicals or radiation
    ■ Can also occur when a DNA polymerase or an RNA polymerase makes a mistake
    ■ RNA polymerases have proofreading abilities, but RNA polymerases do not
  •  Error in DNA not a problem unless that gene is expressed AND the error causes a change in the gene product

➢ Base Substitution

  •  Point mutations result when a single nucleotide is replaced for another
  •  Nonsense mutation
    ■ Cause original codon to become a stop codon, which results in early termination of protein synthesis
  •  Missense mutation
  •  Cause original codon to be altered and produce a different amino acid
  •  Silent mutations
    ■ codon that codes for the same amino acid is created and therefore does not
    change the corresponding protein sequence
  •  Frameshift mutations
    ■ insertions/deletions result in the gain or loss of DNA or a gene
    ● Can have devastating consequences during translation
  • results in a change in the sequence of codons used by the ribosome
  •  Duplications
    ■ Extra copy of genes
    ■ Caused by unequal crossing-over during by meiosis or chromosome
    ■ ,ay result in new traits as one copy may evolve a new function
    ○ Inversions
    ■ Changes occur in the orientation of chromosomal regions
    ■ May cause harmful effects if the inversion involves a gene or an important regulatory sequence
  •  Translocation
    ■ 2 different chromosomes break and rejoin in a way that causes the DNA sequence to be lost, repeated, or interrupted
Scroll to Top