Weekly Study Guide 7
Last revised: Tuesday, October 1, 2002

A. Overview for this week.

This will be the last week devoted to our study of cells – the following week’s focus will shift to animal anatomy and physiology, which will be a welcome change for many!

Our focus this week will be DNA, RNA, and protein synthesis. These days the notion "DNA RNA protein" is a grade school mantra, and I expect you all to be familiar with the basic notion that DNA encodes amino acid sequence information by a triplet codon scheme. Our study will be a bit more in depth about the mechanics of this process.

The history of the discovery of DNA is fascinating – how could so many people have ignored DNA for 50 years, once it was discovered in 1905 that chromosomes were the carriers of heredity? We will explore a few milestone experiments in order to understand what it took to bring about the discovery of DNA’s primary importance.

We will then focus on how DNA is replicated, how RNA is transcribed, and how polypeptides are translated. Lots of details here – I strongly recommend spending some time with the excellent animations and online study tools listed on our web pages and at the Campbell website in order to make this material more understandable.

If time permits, we will end with a brief look at the Human Genome Project, one of the most massive scientific collaborations in history. This is the time to read the booklet “Understanding the Human Genome Project” (UHGP booklet), that came with your text.

B. Lecture Topics and Assigned Reading.

Fri. 11 Oct.
DNA replication
RNA transcription
Ch. 16
Ch. 17
Mon. 14 Oct.
Fall Holiday – no classes today
Wed. 16 Oct.
Protein Synthesis and the Genetic Code
Human Genome Project
Ch. 17
UHGP booklet
Fri. 18 Oct.
Exam #2

C. Take the online Self-Quizzes associated with these lectures.

See the link at bottom of lecture note web pages.

D. Visit Campbell Website. Do assigned activities.

Ch. 16 Ch. 17
E. Take Online WebCT Quiz 7-- covers text Chapters 16 & 17

Online quiz 7 will become available at 8 a.m. on Tuesday, Oct. 15, and remain available until 8 a.m. on Wednesday, Oct. 16. At some time during this 24 hour time window you must log in to your WebCT account and take the quiz. Quiz deadlines are firm and will not be extended for any reason, so please don’t ask – consult the syllabus if you have any questions about timing, grades, and number of quizzes you are required to take.

You will be allowed 12 minutes to complete the 10 questions. The quiz is “open book” – you are allowed to use your text and notes. However, you must take the quiz by yourself, not with the assistance of another person. Once you have completed your quiz, you will be able to see your grade. If you wish to retake a quiz on this material, you may do so once, as long as you are still within the 24 hour time window – in that case, your quiz grade will be the higher of the two quiz grades.

Each quiz is generated randomly from a large database of questions. As a result, no two quizzes will be identical, and it is quite possible that many if not all of the questions you would see in comparing two different quizzes will be entirely different. Each quiz will cover only the material from the assigned chapters – e.g., Quiz 7 will be based entirely of questions drawn from chapters 16 and 17.

F. Consult the study questions below as you read the text.

Chapter 16
  1. Scientists knew that chromosomes carried genes as early as 1905. Why did it take until 1953 for the structure of DNA to be understood?
  2. Explain what each of the following scientists contributed to the “story of DNA”: (a) Griffith, (b) Avery et al, (c) Hershey & Chase, (d) Chargaff, (e) Watson & Crick
  3. Review the basic structure and nomenclature for nucleotides, including: which bases are purines, which bases are pyrimidines, difference between ribose and deoxyribose, variety of mono-, di-, and tri-phosphate forms. What is the difference between dATP and ATP, for example? Between CMP and dCDP?
  4. How many phosphates are present in the nucleotides from which DNA is synthesized? How many phosphate molecules are present per nucleotide in a DNA chain?
  5. Identify the role of each of the following proteins in DNA replication: DNA polymerase, helicase, DNA primase, DNA ligase, Okazaki fragments. (see Fig. 16.16).
  6. What is meant by “antiparallel strands” in DNA? What restriction does this place on replication?
  7. Note that, because the energy for adding new nucleotides to DNA comes from hydrolysis of phosphate bonds, it is only possible to add new nucleotides to a DNA (or RNA) strand at its 3’–terminus. Thus all growth of nucleic acids occurs at the 3’-end; another way of saying this is that new DNA (and RNA) chains are synthesized in the 5’ to 3’ direction. Using this fact, explain what is meant by a “lagging strand” in DNA replication. What is meant by “leading strand”.
  8. DNA polymerase enzymes also carry out proofreading and repair functions, including the excision of incorrectly paired bases and reinsertion of new DNA -- see fig. 16.17. What is the sequence of steps needed to accomplish "excision repair"? How many enzymes are needed? Name them.

Chapter 17
  1. How much DNA is there in a bacterial cell? a human cell? How many proteins could be encoded if all this DNA coded for protein sequences? Approximately what % of this DNA actually codes for proteins sequences?
  2. What is meant by “transcription”? What molecules are needed for this to occur?
  3. What is a promoter?
  4. What are the 3 types of RNA, and what role does each play?
  5. What is meant by “translation”? Where does this occur in the cell? What molecules are needed for this to occur?
  6. A molecule of m–RNA has the following structure:
    ...... A A A U G G G G G U C U U U G U G C U A G G G U G A U U G .......


    Write the sequence of the translated protein (use the genetic code below)
    Note: where is the “start” codon? Does this protein have a “stop” codon?

    The Genetic Code
    U
    C
    A
    G

    U
    UUU – phe
    UUC – phe
    UUA – leu
    UUG – leu
    UCU – ser
    UCC – ser
    UCA – ser
    UCG – ser
    UAU – tyr
    UAC – tyr
    UAA – stop
    UAG – stop
    UGU – cys
    UGC – cys
    UGA – stop
    UGG – trp
    U
    C
    A
    G

    C
    CUU – leu
    CUC – leu
    CUA – leu
    CUG – leu
    CCU – pro
    CCC – pro
    CCA – pro
    CCG – pro
    CAU – his
    CAC – his
    CAA –gln
    CAG –gln
    CGU – arg
    CGC – arg
    CGA – arg
    CGG – arg
    U
    C
    A
    G

    A
    AUU – ileu
    AUC – ileu
    AUA – ileu
    AUG – start/met
    ACU – thr
    ACC – thr
    ACA – thr
    ACG – thr
    AAU – asn
    AAC – asn
    AAA – lys
    AAG – lys
    AGU – ser
    AGC – ser
    AGA – arg
    AGG – arg
    U
    C
    A
    G

    G
    GUU – val
    GUC – val
    GUA – val
    GUG – val
    GCU – ala
    GCC – ala
    GCA – ala
    GCG – ala
    GAU – asp
    GAC – asp
    GAA – glu
    GAG – glu
    GGU – gly
    GGC – gly
    GGA – gly
    GGG – gly
    U
    C
    A
    G


  7. What is the role of a ribosome? Where are they found? Are there different ribosomes to make different proteins?
  8. What do activating enzymes (technically, “aminoacyl tRNA synthetases) accomplish? Approximately how many of them are there?
  9. “Codons” represent a series of 3 bases in DNA or RNA that specify a single amino acid. “Anticodons” are found on transfer RNA molecules. Theoretically, if there are 64 different codons, how many anticodons must there be?
  10. Note that the “start” codon AUG is also the first amino acid of a protein, methionine (abbreviated met). Does this mean that every protein should start with met?
  11. Note that the “stop” codons do not specify any amino acid but instead cause termination of protein growth. What are the 3 stop codons?
  12. The process of protein synthesis is pretty complicated, and is normally discussed in 3 steps: initiation, elongation, and termination — see Figs. 17.15-17. mRNA attaches to a ribosome; tRNA molecules bring amino acids into the ribosome, match up their anticodons with appropriate codons on the mRNA, and locate amino acids at the appropriate positions. Note that there are only two sites on the ribosome at which tRNA can bind. Why are these called A and P? What binds to each of these two sites?
  13. Besides ribosomes, m-RNAs and AA-tRNAs, what other factors are required for protein synthesis? What is a termination factor? When is it required?
  14. What is a polyribosome?
  15. How is protein synthesis different between prokaryotes and eukaryotes?
  16. What is an exon? an intron? a spliceosome? Be sure you understand Fig. 17.10.
  17. What is a ribozyme? Give two examples.
  18. What is a mutation? Give an example of a point mutation, an insertion, and a deletion mutation.
  19. What are some common causes of mutations?
  20. In the following list, identify which components are required for DNA replication (label “1”), transcription (label “2”), and translation (label “3”).
(a) DNA polymerase
(b) t–RNA
(c) elongation factors
(d) m–RNA
(e) ribosomes
(f) primase
(g) helicase
(h) “AUG” codon
(i) RNA polymerase
(j) ATP, CTP, GTP, UTP
(k) amino acids
(l) initiation factor
(m) dATP, dCTP, dGTP, dTTP
(n) release factor
(o) promoter

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