Answers to many of these questions can be found on the "Answers to End-of-Chapter Questions" page at the text website.

For feedback, post possible answers and ideas in the folder "Text 'Review' and 'To Think About' Questions" in the Biology Chat Section of Web Crossing.

• The Graphics Gallery at Access Excellence (lots of neat illustrations here).
• BioTech's Dictionary. A biotechnology reference tool from Indiana University
• Transcription and Translation from the University of Texas, Austin.
• MIT's Central Dogma Directory
• Human Biology (BIOL121) from the University of Virginia with lots of nice slides.
• BioTech's "An Introduction to Translation" by Indiana University
• What are genes? ( A good review of terminology!)

1. Describe what is meant by the semi-conservative replication of DNA, and explain the roles of DNA, unattached DNA nucleotides, and enzymes in this process.

2. Draw a diagram, create a concept map, or write a paragraph that explains the relationships among these terms:

   chromosome	allele	gene expression
   trait	DNA	RNA polymerase
   messenger RNA	transfer RNA	ribosomal RNA
   codons	anticodons	ribosomes
   transcription	translation	RNA processing
   amino acids	peptide bonds	polypeptides
   primary stucture	secondary structure	tertiary structure
   quaternary structure	compact disks	cassette tapes

3. Explain how the sequence of DNA nucleotides for a specific allele, such as the allele for Cystic Fibrosis, is related to the production of a specific membrane protein.

4. Explain transcription and translation, and the roles of RNA polymerase, messenger RNA, transfer RNA, ribosomal RNA, and ribosomes in carrying out these two processes.

5. Describe the basic changes in substrate molecules that may occur as they are converted to products by reactions catalyzed by the action of enzymes.

• Each time a cell divides, its DNA must replicate DURING THE S PHASE OF THE CELL CYCLE, so that each daughter cell receives the same set of genetic instructions.

• Production of identical copies relies on complementary base pairing (A-T and C-G)

• Replication is semi-conservative. Each new double helix has one parent strand and one new strand.

• Many different enzymes are involved.

• At 50 bases/sec, human DNA would require 3.8 years for one replication, so replication begins at multiple sites within each chromosome.

• DNA polymerase "proofreads" as it goes, excising mismatched bases and inserting correct ones.
  • An introduction to nucleic acid sequences from BioTech at Indiana University

  • A View of a DNA Molecule from Access Excellence

  • Semi-Conservative DNA Replication movie (This should help with this concept)

  • The collaboration of proteins from Access Excellence - (more detail than you really need, but sometimes you need a little more)

• The flow of genetic information from DNA to RNA to protein. DNA codes for the production of RNA, which in turn codes for the production of protein.
  • How are genes linked to disease? (from Access Excellence)

  • *"Central Dogma" from Access Excellence

  • *DNA replication & Protein Synthesis Illustration from the University of Texas at Austin

  • Diagram of a Retrovirus

    *Note that DNA REPLICATION IS NOT part of protein synthesis!!!!

• Transcription occurs in the nucleus.

• Transcription is the synthesis of a molecule of RNA that is complementary in nucleotide sequence to one side (the transcribed side) of a section of the DNA double helix that would be an allele for a particular trait.
  • Remember the compact disk analogy for chromosomes?

  • The section of DNA being transcribed is an allele - analogous to one "track" on one of your 46 CDs.

  • A copy of the information in the allele is produced in the form of a messenger RNA molecule.

  • The information is copied, but is in a complementary form
    • (A in the RNA instead of T in the DNA).

    • (U not T in the RNA instead of A in the DNA).

    • (C in the RNA instead of G in the DNA).

    • (G in the RNA instead of C in the DNA).

  • Transcription, producing RNA, is analogous to the production of a short cassette tape from one track on the CD.

  • The digital information on the CD is transfered to the cassette, but in magnetic form.

• Transcription factors are protein molecules that determine which genes are expressed in which tissues at which stages of development. The promotor, a control sequence near the start of the gene, attracts RNA polymerase and transcription factors. It tells the RNA polymerase where to begin transcription on the transcribed strand of the DNA double helix.
  • This is sort of like setting the program on your CD player for a particular track.

• Enzymes unwind the DNA strand, and RNA polymerase builds the RNA chain using the transcribed strand of the DNA double helix as a template.

  
  This animated graphic is from the University of Texas, Austin

  • The orange and blue strand is the double helical DNA molecule.
  • The blue portion is the section of DNA being transcribed (again and again and again...)
  • The light blue moving ball is a molecule of RNA polymerase
  • The yellow strands are single stranded molecules of RNA

• RNA undergoes processing in the nucleus after transcription
  • noncoding sequences called introns are removed, and the 5' and 3' ends are modified

  • a "cap" is added to the 5' end of the molecule, and a "poly-A tail" is added to the 3' end.

  • Processing of the primary RNA transcript from the University of Arizona (showing the 5' cap and 3' poly-A tail)

  • This is like editing the cassette tape to filter out unwanted noise copied from the CD.

• Translation (Three Stages) Occurs in the Cytoplasm at the Ribosomes
  (Movie from the University of Virginia)
  • Initiation: the first mRNA codon AUG forms a complex with an initiator tRNA (carrying the amino acid methionine) and the small ribosomal subunit. The large ribosomal subunit then joins this complex to begin the next stage.
    • The Cassette Tape (mRNA) is placed in the Cassette Tape Player (ribosome) and the start of the music (AUG) is found.

  • Elongation: the stepwise addition of amino acids to a growing polypeptide chain. The ribosome moves along the mRNA one codon at a time, transferring new amino acids to the growing polypeptide chain via peptide bonds.
    • The player plays the cassette tape producing a sequence of 20 different tones (amino acids).

  • Termination: elongation stops at an mRNA stop codon, and the new polypeptide is released. The ribosome breaks into its large and small subunits, releasing the new protein and the mRNA.
    • When the cassette tape reaches the end of the music (stop codon) it rewinds and starts playing the tape again (the mRNA attaches to a new ribosome and translation starts again).

• The Genetic Code (MESSENGER RNA)
  (from the University of Virginia)
  • Three consecutive bases (a codon) in a MESSENGER RNA molecule code for one amino acid.

  • The code is redundant, with some amino acids having more than one codon (See Leu in the codon chart).

  • The first and second bases of each codon are more important than the last.

  • The codon AUG starts translation, and the codons UGA, UAA, and UAG stop translation.

• The Three Types of RNA
  • Messenger RNA (mRNA) is a complimentary copy of one strand (the transcribed strand) of a section of a DNA molecule making up an allele. It acts as a messenger to carry information stored in the DNA in the nucleus to the cytoplasm where the ribosomes on the E. R. can translate it to synthesize protein molecules. Each three mRNA bases in a row forms a codon that specifies a particular amino acid.

  • Transfer RNA (tRNA) is small and has a very specific secondary and tertiary structure such that it can bind an amino acid at one end and mRNA at the other. It carries each amino acid to the ribosome. tRNA contains a sequence of 3 nucleotide bases at one end of the molecule called an anticodon. This anticodon is complementary to a particular codon of an mRNA molecule.

  • Ribosomal RNA (rRNA) is one of the structural components of a ribosome. Ribosomes structurally support and catalyze protein synthesis. In eukaryotes, a ribosome has two subunits (large and small), containing 82 proteins and four rRNA molecules altogether (see Fig. 16.8, text).

• Transcription and Translation in Review
  • Relationship among DNA, mRNA, and amino acid sequences from the University of Virginia
    • In this illustration the Transcribed strand of the DNA is the upper line of letters (TAC CAC, etc).

    • Note that the mRNA sequence looks very much like the Non-Transcribed side of the DNA except, of course, that there are Us in the RNA and Ts in the DNA

  • RNA transcript of the beta-globin gene and corresponding amino acid sequence, from the University of Virginia
    • Here you can see the entire transcript (new mRNA molecule) just as it is produced by the RNA polymerase from the transcribed strand of the DNA double helix of the allele.

    • The introns, magenta colored sections, are cut out by enzymes in the nucleus.

    • The exons , the black sections, are spliced back together by other enzymes and sent out to the ribosomes for translation.

    • The abreviations of the amino acids are lined up with the codons in the exons so you can see the primary structure of the protein beta-globin.

• Transcription and Translation - Graphic Representation from the University of Virginia

• Biol 121, Human Biology, at the University of Virginia.

• Protein Synthesis from Access Excellence: (This is the same figure Ed asked you to print out last lecture!

  .

• Additional changes are made to the protein before it can perform its function.
  • Protein Folding (A review of last lecture)
    
    (See Fig. 3.28, text, for examples)
    • Primary Structure: The order (sequence) of amino acids in the polypeptide chain.

    • Secondary Structure: The barrels, loops, coils, sheets, or corkscrews created when amino acids close to each other in the primary sequence interact.

    • Tertiary Structure: The 3-D folded structure of the polypeptide chain. Remember that a protein's conformation (structure) determines its function.

    • Quaternary Structure: The interconnections and organization of two or more polypeptide chains, if present.
      • MIT's Protein Structure

      • Protein Molecules, a link from last lecture.

  • Some proteins are Enzymes which:
    • Act as catalysts to reduce the energy needed to make or break chemical bonds in molecules.

    • Have active sites with specific shapes and chemical properties into which specific substrate molecules fit.

    • May break apart molecules

    • May join two or more molecules

    • May re-arrange molecules

    • May require the energy of ATP or NAD

    • May require an organic helper molecule (a coenzyme)

    • May require an inorganic helper molecule (a cofactor)

    • Loose their activity if thy are denatured

  Take me home, right now!