Chapter 16: Review Molecular Basis of Inheritance

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Chapter 16 ReviewMolecular Basis of Inheritance

• Search for genetic material led to DNA
• Discovery- DNA double helix
• DNA replication Basics
• DNA repair

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Chapter 17 From Gene to Protein

• Study of metabolic defects provided evidence that
  genes specify proteins
• Transcription translation are main processes
  linking gene to protein.
• Genetic code nucleotide triplets specify amino
  acids

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• Transcription is the DNA-directed synthesis of
  RNA
• Signal peptides target some eukaryotic
  polypeptides to specific destinations in the cell
• RNA plays multiple roles in the cell
• Compare protein synthesis in prokaryotes
  eukaryotes.

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• A point mutation can affect the function of a
  protein
• Ask again, what is a gene?

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Study of Metabolic Defects Provided Evidence that
Genes Specify Proteins

• Archibald Garrod (1909) proposed relationship
  between genes proteins (alkaptonuria, dark
  urine)
• George Beadle Edward Tatum (1930s) demonstrated
  the relationship between genes enzymes while
  studying a bread mold with mutants.

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How Do Genes Control Metabolism

• Beadle Tatum
• Red bread mold (maybe you know it)
• Wild-type strain has minimal requirements.
• Multi-step pathway to synthesize the amino acid
  arginine from a precursor
• Three classes of mutants unable to metabolize
  arginine.

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Neurospora - Red Bread Mold
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• They concluded that each mutant was defective in
  a single gene coding for one enzyme.
• This lead to the one gene-one enzyme hypothesis
  the function of a gene is to dictate the
  production of a specific enzyme.

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Modified Idea

• This idea was modified to be one gene-one
  polypeptide hypothesis because not all proteins
  are enzymes (keratin, insulin).
• Many proteins are made of several polypeptides
  (hemoglobin, 2 chains).

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Transcription Translation Two Main Steps from
Gene to Protein

• Genes are the instructions for making specific
  proteins, but a gene does not build a protein
  directly.
• The bridge between genetic information and
  protein synthesis is RNA, ribonucleic acid (Chap.
  5).

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DNA RNA Both Polymers

• Both RNA DNA are nucleotide polymers with two
  main differences deoxyribose of DNA has one less
  hydroxyl group than ribose (sugar) the other
  difference is the nitrogenous base-thymine (T) is
  unique to DNA uracil (U) unique to RNA.

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DNA RNA Structural Differences
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• Flow of information - gene to protein, is
  described in linguistic terms because both
  nucleic acids and proteins have specific
  sequences of monomers, much as specific sequences
  of letters communicate information in the written
  word.

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• DNA/RNA - monomers are the four types of
  nucleotides (nitrogenous bases differ) that are
  100s or 1000s of nucleotides long, each gene
  having a specific base sequence.

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• A protein has monomers in a particular linear
  order, but the monomers are......?

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Amino Acids

• Amino acids..20 of them.
• Thus, nucleic acids proteins contain
  information written in two different chemical
  languages....

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• Getting from one to the other requires two major
  stepsTranscription and Translation

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Transcription

• Transcription is the synthesis of RNA under the
  direction of DNA (template...recall replication).
  Both nucleic acids use the same monomeric
  language, the information just has to be
  transcribed (copied) from one molecule to another.

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• The RNA molecule made according to the DNA
  template is a transcript of the genes
  protein-building instructions.

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• This RNA is called mRNA (messenger RNA), which
  functions as a genetic message from DNA to the
  protein-synthesizing machinery.

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• Translation is the actual synthesis of a
  polypeptide, which occurs under the direction of
  mRNA.

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• There is a change in language from the base
  sequence of an mRNA into the amino acid sequence
  of a polypeptide.

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• Ribosomes are the sites of translation, which are
  made of numerous enzymes other agents that
  facilitate the orderly linking of amino acids.

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Prokaryote/Eukaryote Difference?

• Bacteria lack a nuclei, so DNA is not segregated
  from ribosomes, etc.
• Thus, transcription translation are coupled,
  with ribosomes attaching to the leading end of an
  mRNA molecule while transcription is still
  ongoing. (Fig. 17.2, CD).

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Prokaryotic Cell
No Nucleus
Immediate Translation
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RNA Processing
Nucleus
Eukaryotic Cell
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• DNA RNA Protein

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Genetic Code Nucleotide Triplets Specify Amino
Acids

• Only four nucleotides code for 20 amino acids.

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Codon

• Three nucleotide words are called codons.
• Codonthree-nucleotide sequence in mRNA that
  specifies which amino acid will be added to a
  growing polypeptide or that signals termination.
• Codon is basic unit of genetic code.

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Recall.......

• Genes are not directly translated into amino
  acids, but are first transcribed as codons into
  mRNA.
• Only one strand is transcribed, the other
  non-template strand serves as a parental strand
  for making a new template when DNA replicates.

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• An mRNA is complementary to the DNA template from
  which it is transcribed, for example, the DNA
  sequence CCG is the codon for glycine, the
  complementary mRNA transcript is GGC. Uracil
  substitutes for thymine pairs with adenine
  (Fig. 17.3).

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Triplet Code
DNA
mRNA
Amino Acid
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Fig. 17.4 Triplet code.

• Each mRNA codon specifies which one of the 20
  amino acids will be incorporated into a
  corresponding position in a polypeptide.
• The number of nucleotides making up a genetic
  message is 3 times the number of amino acids.

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Cracking the Genetic Code

• By the mid-1960s all 64 codons were known. Figure
  17.4 is the dictionary of the genetic code.

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GENETIC CODE
Stop UAA UAG UGA
AUG Met. Start
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Factoid

• AUG that codes for methionine (Met, start signal
  or initiation codon) is sometimes removed
  subsequently.

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• There is redundancy in the code....several codons
  for one amino acid, but there is no ambiguity
  (same codon for two amino acids). Codons for the
  same amino acid may differ only in the third base
  of the triplet.

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Reading Frame

• Reading frame correct grouping of adjacent
  nucleotide triplets into codons that are in the
  correct sequence on mRNA. nonoverlapping
  three-letter words.

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Reading frame

• THE BIG RED CAT ATE THE BIG BAD FAT
  RAT.
• HEB IGR EDC ATA TET HEB IGB ADF ATR AT-

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• My codon is A D D.
• Attention
• Deficit
• Disorder
• What is your codon?

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The Genetic Code

• The genetic code is nearly universal - a language
  that is shared across all of life meaning it must
  have been operating very early in the history of
  life.

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Transcription Up CloseTranscription is the
DNA-DirectedSynthesis of RNA

• RNA polymerases pry apart the two DNA strands
  hook together the RNA nucleotides as they base
  pair along the template beginning at the 3 end.

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• DNA that is transcribed into an RNA molecule is
  the TRANSCRIPTION UNIT.

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Transcription Up Close

• Prokaryotes have one RNA polymerase. Eukaryotes
  have three.
• mRNA synthesis-RNA polymerase II
• Transcription steps 1) polymerase binding
  initiation 2) elongation 3) termination

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RNA Polymerase Binding Initiation

• RNA polymerases bind to DNA regions called
  PROMOTORS.

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• Promoter initiation site dozens of
  nucleotides upstream from initiation site.
  e.g. TATA box (eukaryotes) are 25 bases
  upstream.

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• TRANSCRIPTION FACTORS - aid polymerases in
  finding promotor regions on DNA (sometimes attach
  before polymerase can bind).

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Elongation

• RNA polymerase II untwists DNA one turn (helix)
  at a time exposing 10 bases for pairing of RNA
  nucleotides at the 3 end.

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• mRNA peels away as the noncoding strand reforms
  the double helix.

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• A single gene can be transcribed simultaneously
  by several polymerase IIs so it can produce
  proteins faster (more copies of mRNA).

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Termination

• RNA polymerase transcribes until termination site
  is reached (AAAAAA in eukaryotes).
• Play CD 2

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Figure 17.6
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Figure 17.7
Initiation of Transcription at a Eukaryotic
Promoter
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Eukaryotic Cell Modify RNA after Transcription

• Alternation of mRNA Ends
• Split Genes and RNA Splicing
• Ribozymes

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RNA Processing Both ends (5 3) are
modified, then cut apart spiced together again

• Alteration of mRNA ends - in the nucleus- 5
  Cap protects mRNA is an attach here signal
  for small ribosomes.

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• - 3 Poly-A tail (several hundred adenines) for
  protection transport from nucleus to cytoplasm.

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RNA Processing Add Cap Tail
3Tail
5Cap
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RNA Processing

• RNA splicing - Average DNA molecule is 8000
  bases, RNA in nucleus is same length, but 1200
  nucleotides to code for protein of 400 amino
  acids.

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• What happened to the 6,800 nucleotides between
  the nucleus and cytoplasm....?

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RNA Processing

• INTRONS - intervening noncoding segments of DNA
  are transcribed then removed.

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• EXONS - are coding regions that are express
  eventually (translated into proteins).
• RNA splicing occurs for tRNA rRNA mRNA. (see
  Figure 17.9).

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RNA Processing Splicing
Transcription
Introns Excised
Exons Spliced
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Play CD
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Synthesis of ProteinTranslation Up Close (p. 304)

• In the Process of Translation a cell interprets a
  genetic message builds a protein.
• The message is a series of codons along the mRNA
  molecule
• The interpreter is another type of RNA - TRANSFER
  RNA (tRNA).

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TRANSFER RNA

• tRNA transfers amino acids from the cytoplasms
  amino acid pool to the ribosome.
• Cell keep the pool stocked with 20 amino acids it
  makes or takes up from the surrounding solution.

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• Some 45 different tRNA molecules associate with
  particular mRNA codons that code for amino acids.

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Translation Up Close

• On one end is a tRNAs particular amino acid, on
  the other end is a base triplet called an
  ANTICODON
• The anticodon binds according to the base-pairing
  rules to a mRNA codon.
• Ribosomal enzymes join amino acids into a chain.

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Transfer RNA

• tRNAs are transcribed in the nucleus from DNA
  templates (nucleus) then travel to cytoplasm for
  translation where they are used repeatedly.

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• Some tRNAs have anticodons that recognize two or
  more codons. The third base pairings (between
  anticodon mRNA) are not as strict.

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• This relaxation of base-pairing rules is called
  WOBBLE. Explains synonymous codons for certain
  amino acids.

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• See Figure 17.13 for aminoacyl-tRNA synthase
  joining a tRNA to an amino acid......

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Ribosomes

• Ribosomes facilitate the specific coupling of
  tRNA anticodons with mRNA codons during protein
  synthesis.
• Ribosomal unit proteins (large small subunit)
  ribosomal RNA (rRNA)

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Building a Polypeptide

• InitiationgtElongationgt Termination

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Building a Polypeptide

• Initiation mRNA tRNA (with amino acid) two
  ribosomal subunits GTP (energy).

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Initiation of Translation
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Building a Polypeptide

• Elongation Codon recognition (GTP) gt Peptide
  bond formation (peptidyl transferase) release
  of amino acid from tRNA

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Elongation of Translation
Codon Recognition
Peptide Bond Formation
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Building a Polypeptide

• Translocation tRNA dissociates from
  ribosome....mRNA ribosome move in unison
  (ratchet-like).

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Elongation of Translation
A Site
P Site
Translocation
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Building a Polypeptide

• Termination Elongation until TERMINATION CODON
  reached (UAA, UAG, UGA - not amino acid
  codons)Release factor hydrolyzes the completed
  polypeptide from the tRNA, freeing the
  polypeptide from the ribosome.
• See Figures 17.14 - 17

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Termination of Translation
Free Polypeptide
Ribosome Dissociation
Termination Codon
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Play CD
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Building a Polypeptide

• POLYRIBOSOMES - more than one ribosome
  translating on same mRNA molecule (Figure 17.18
  in book).

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Signal Peptides

• Free (cytosol) bound (to endoplasmic reticulum)
  ribosomes - Free - proteins in cytosolBound -
  membrane proteins proteins to be secreted.

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• SIGNAL SEQUENCE - on peptide enables ribosome to
  attach to receptor site on ER membrane (signal
  seq. is eventually removed).

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Signal Mechanism for Targeting Proteins
Signal Sequence
Signal Recognition Particle
Receptor Site
Endoplasmic Reticulum
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Types of RNA in a EukaryoteSee Table 17.1

• Messenger RNA
• Transfer RNA
• Ribosomal RNA
• Primary transcript
• Small nuclear RNA
• Signal recognition particle

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Mutations

• MUTATIONS are changes in the genetic makeup of a
  cell.

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• POINT MUTATIONS - chemical changes in just one
  nucleotide in a single gene. e.g. gene in gamete
  with point mutation may be passed on to next
  generation (genetic disorder)

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Types of Mutations

• SUBSTITUTIONS base-pair is replaced by another
  pair of nucleotides. Net result is a MISSENSE
  mutation that still codes for an amino acid.

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• May not be a problem unless it is a termination
  codon (NONSENSE MUTATION).

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Types of Mutations

• INSERTIONS DELETIONS addition or loss of a
  nucleotide pairs in a gene. This more disasterous
  as may throw off reading frame causing a
  FRAMESHIFT MUTATION.

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• Unless three nucleotides are added or deleted, or
  the mutation is near the end of the gene, the
  protein is likely to be nonfunctional.

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Molecular Basis of Sickle-Cell Disease A Point
Mutation
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Categories Consequences of Point Mutations
(Fig. 17.22)
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Mutagens

• MUTAGENS - physical or chemical agents that
  interact with DNA to cause mutations (e.g.
  x-rays, UV light).

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• AMES TEST - for mutagenic strength of chemicals
  (pesticides, drugs for mutagenic cancer-causing
  potential) see text.

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See Figure 17.23Transcription Translation