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Bio 107 Fall 1999 Study Guide on Chs. 16, 17 Prof. Terry

Ch. 16. DNA.
  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. Know 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 a nucleotide? A nucleoside? What is the difference between dATP and ATP? 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 also carries out proofreading and repair functions, including the excision or incorrectly paired bases and reinsertion of new DNA

Ch. 17. RNA, protein synthesis, and the genetic code.
  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 at the end of this handout)
    Note: where is the "start" codon? Does this protein have a "stop" codon?
  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– 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


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