1' Give early experimental evidence that implicated proteins as the links between genotype and pheno

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1. Give early experimental evidence that
implicated proteins as the links between genotype
and phenotype.

• Inherited instructions in DNA direct protein
  synthesis, thus proteins are the links between
  genotype and phenotype
• Garrod suggested that genes dictate phenotypes
  through enzymes that catalyze reactions ?

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2. Describe Beadle and Tatums experiments with
Neurospora, and explain the contribution they
made to our understanding of how genes control
metabolism.

• Relationship between genes and enzymes
• Wild type (bread mold) can survive on minimal
  medium ? looked for mutants or auxotrophs that
  could not live because they cant synthesize
  molecules
• Results ? one gene one enzyme hypothesis ? the
  function of a gene is to dictate the production
  of a specific enzyme ?

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3. Distinguish between one gene-one enzyme
hypothesis and one gene-one polypeptide, and
explain why the original hypothesis was changed.

• One gene one enzyme
• Gene codes for a specific enzyme

• One gene one polypeptide
• Most enzymes are proteins
• Many proteins are not enzymes
• Proteins that are not enzymes are still gene
  products
• Many proteins are comprised of 2 or more
  polypeptide chains, each chain specified by a
  different gene ?

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4. Explain how RNA differs from DNA.

• Both are nucleic acids polymers of nucleotides
• RNA is different from DNA
• - the 5 carbon sugar is ribose not deoxyribose
• - the nitrogen base is uracil not thymine ?

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5. Briefly overview, in your own words, how
information flows from gene to protein.

• Two processes transcription and translation
• Transcription ? the synthesis of RNA using DNA as
  a template
• Translation ? the synthesis of a polypeptide
  which is directed by mRNA
• DNA ? RNA ? protein

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6. Distinguish between transcription and
translation.

• Transcription ? is the synthesis of RNA under the
  direction of DNA
• Translation ? the actual synthesis of a
  polypeptide, which occurs under the direction of
  mRNA ?

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7. Describe where transcription and translation
occur in prokaryotes and in eukaryotes explain
why it is significant that in eukaryotes,
transcription and translation are separated in
space and time.

• Prokaryotes ? lack nuclei so DNA is not
  segregated from ribosomes or the protein
  synthesizing machinery (occurs in rapid
  succession)
• Eukaryotes ? have nuclear envelopes that
  segregate transcription in the nucleus from
  translation in the cytoplasm mRNA (the
  intermediary) is modified before it moves from
  the nucleus to the cytoplasm where translation
  occurs ?

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8. Define codon, and explain what relationship
exists between the linear sequence of codons on
mRNA and the linear sequence of amino acids in a
polypeptide.

• Codon ? a 3-nucleotide sequence in mRNA that
  specifies which amino acid will be added to a
  growing polypeptide or that signals termination ?
  the basic unit of the genetic code
• Genes are not directly translated into amino
  acids but are first transcribed as codons into
  mRNA ?

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9. List the three stop codons and the one start
codon.

• Start?AUG
• Stop?UAA
• UAG
• UGA

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10. Explain in what way the genetic code is
redundant and unambiguous.

• Redundant ? two or more codons differing only in
  their 3rd base can code for the same amino acids
  (UUU
  UUC phenylalanine)
• Unambiguous ? codons code for only ONE amino
  acids
• (UUU ONLY codes for phenylalanine) ?

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11. Explain the evolutionary significance of a
nearly universal genetic code.

• It indicates that the code was established very
  early in lifes history

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12. Explain the process of transcription
including the three major steps of initiation,
elongation, and termination.

• Initiation ? a RNA polymerase attaches at a
  specific region of DNA called the promoter, and
  begins transcription (often called the TATA box)
• Elongation ? as RNA polymerase moves along the
  DNA, 10 20 bases are exposed at a time for
  pairing with RNA nucleotides
• Termination ? transcription proceeds until RNA
  polymerase transcribes the termination sequence ?

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13. Describe the general role of RNA polymerase
in transcription and explain how it recognizes
where to begin.

• RNA polymerases bind at the promoter and in
  eukaryotes they need transcription factors to
  recognize them
• The enzyme separates the 2 DNA strands at the
  initiation site and transcription begins ?

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14. Specifically, describe the primary functions
of RNA polymerase II.

• It untwists and opens a short segment of DNA
  exposing about 10 nucleotide bases ? one of the
  exposed DNA strands is the template for
  base-pairing with RNA nucleotides
• It links incoming RNA nucleotides to the 3 end
  of the elongating strand, thus, RNA grows one
  nucleotide at a time in the 5 to 3 direction ?

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15. Distinguish among mRNA, tRNA, and rRNA.

• mRNA ? messenger RNA what the DNA nucleotide
  sequence is transcribed into
• tRNA ? transfer RNA
• rRNA ? ribosomal RNA translation occurs on
  ribosomes, complex particles composed of rRNA and
  protein that facilitate the orderly linking of
  amino acids into polypeptide chains ?

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16. Describe the structure of tRNA and explain
how the structure is related to the function.

• tRNA is transcribed from DNA templates, made in
  the nucleus and travels out into the cytoplasm
• Used repeatedly picks up its designated amino
  acid in the cytosol, deposits it at the ribosome,
  and leaves to pick up another
• Consists of a single RNA strand that is only
  about 80 nucleotides long, has a protruding end
  which serves as the attachment site for the amino
  acid ?

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17. Given the sequence of bases in DNA, predict
the corresponding codons transcribed on mRNA and
the corresponding anticodons of tRNA.

• DNA
• CTAGGATGCAAATGC
• mRNA
• GAUCCUACGUUUACG
• tRNA
• CUAGGAUGCAAAUGC ?

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18. Describe the wobble effect.

• It is a relaxation of the base-pairing rules
• If one tRNA variety existed for each of the mRNA
  codons that specifies an amino acid, there would
  be 61 tRNAs, there are only 45
• - this is because some tRNAs can recognize two
  or more codons ?

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19. Explain how an aminoacyl-tRNA synthetase
matches a specific amino acid to its appropriate
tRNA describe the energy source that drives this
endergonic process.

• There are 20 types of these enzymes in a cell,
  each specific for an amino acid
• The active site of each enzyme fits only a
  specific combination of amino acid and tRNA
• The synthetase catalyzes the covalent attachment
  of the amino acid to its tRNA in a process driven
  by the hydrolysis of ATP ?

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20. Describe the structure of a ribosome and
explain how this structure relates to function.

• A ribosome is made up of 2 subunits (large and
  small) these are constructed of proteins and
  ribosomal RNA molecules, and are made in the
  nucleolus
• Function is to bring mRNA together with the amino
  acid-bearing tRNAs, therefore they have binding
  sites for mRNA and tRNA ?

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21. Describe the process of translation including
initiation, elongation, and termination and
explain what enzymes, protein factors, and energy
sources are needed for each stage.

• Initiation ? when mRNA, tRNA and the first amino
  acid come together with the ribosome
• - protein initiation factors bring everything
  together to begin (GTP provides energy) ?

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Elongation

• Elongation ? amino acids are added one by one,
  helped by protein elongation factors
• 1. Codon recognition mRNA codon makes a
  hydrogen bond with the tRNA anticodon (requires
  GTP hydrolysis)
• 2. Peptide bond formation a ribozyme catalyzes
  the peptide bond creating a polypeptide which
  then separates from its tRNA
• 3. Translocation the tRNA moves to another
  part of the ribosome, and the next codon to be
  translated steps up finally the tRNA leaves
  (requires hydrolysis of GTP) ?

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Termination

• Termination ? elongation continues until there is
  a stop codon a protein release factor binds and
  adds a water to finish the polypeptide ?

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22. Explain what determines the primary structure
of a protein and describe how a polypeptide must
be modified before it becomes fully functional.

• A gene determines the proteins primary structure
  (its amino acid sequence)
• Primary structure then determines conformation
  changes
• Posttranslational modifications ? chemical
  modification by adding sugars, lipids,
  phosphates, or others ?

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23. Describe what determines whether a ribosome
will be free in the cytosol or attached to rough
ER.

• Free ? suspended in cytosol and mostly synthesize
  proteins that dissolve in the cytosol and
  function there
• Bound ? attached to the cytosol side of the ER
  and make proteins which are secreted from the
  cell (ex insulin)
• - occurs if the growing polypeptide ITSELF cues
  the ribosome to attach to the ER marked by a
  signal peptide, which targets the protein to the
  ER ?

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24. Explain how proteins can be targeted for
specific sites within the cell.

• A signal peptide is recognized by the SRP
  (signal-recognition particle), and this dictates
  where that particular protein will be headed for
  work.
• - as the polypeptide is being synthesized, it
  begins to snake around to where it will be
  located within the cell (ER, mitochondria,
  chloroplast, etc.) ?

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25. Describe the difference between prokaryotic
and eukaryotic mRNA.

• Prokaryotic
• A transcription unit can contain several genes,
  so the resulting mRNA code may code for
  different, but functionally related, proteins

• Eukaryotic
• A transcription unit contains a single gene, so
  the resulting mRNA codes for synthesis of only
  one polypeptide ?

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26. Explain how eukaryotic mRNA is processed
before it leaves the nucleus.

• In eukaryotes, RNA transcripts are modified
  before leaving the nucleus to make functional
  mRNA
• This can happen in two ways
• 1. Covalent alteration of both the 3 and 5
  ends
• 2. Removal of intervening sequences
• Pre-mRNA is what the molecule is called prior
  to this alteration ?

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27. Describe some biological functions of introns
and gene splicing.

• Introns the noncoding segments of nucleic acid
  that lie between coding regions
• Exons segments which are eventually expressed
  through amino acid sequences
• Splicing occurs when the introns are cut out of
  the initial length to transcribe and translate
  the portion that will code for used information ?

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28. Explain why base-pair insertions or deletions
usually have a greater effect than base-pair
substitutions.

• Substitutions ? the replacement of one nucleotide
  and its partner in the complementary DNA strand
  with another pair of nucleotides
• Insertions and deletions ? the additions or
  losses of one or more nucleotide pairs in a gene ?

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29. Describe how mutagenesis can occur.

• Mutagenesis ? the creation of mutations
• - due to errors in DNA replication, repair, or
  recombinations that result in base-pair
  substitutions, insertions, or deletions ?
• The End!

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