ch. 17 from gene to proteindifference in prokaryote and eukaryote protein synthesis prokayotes no...
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Ch. 17 From Gene to Protein
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Essential Question:
How does the genetic information carried in the DNA of genes synthesize proteins that give us our traits?
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Proteins are the link between genotype and phenotype
gene expression = the process by which DNA directs protein synthesis
two stages:transcriptiontranslation
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1909 Archibald Garrodgenes give us the phenotypes via enzymes that catalyze chemical reactions
inherited diseases = inability of a person to make an enzyme
Ex. alkaptonuriablack urine due to alkapton, blackens on
exposure to air most people have enzyme to break it downpeople with alkaptonuria have inherited the
inability to make that enzyme
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Beadle and Tatum mid 1930'sworked with Neurospora crassa (bread mold)
wild type survived on minimal medium
mutants needed complete growth medium (minimal + nutrients and 20 amino acids)
figured out metabolic defect by putting each mutant strain in minimal medium + one nutrient or amino acid
*came to conclusion that one geneone enzyme hypothesis
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Beadle and Tatum experiment
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problem not all proteins are enzymesex. keratin, insulin
came up with new idea:one gene one polypeptide hypothesis
however, some genes code for RNA that never translate into proteins
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Two major steps to go from DNA to Proteins:
I. Transcriptionsynthesis of mRNA from DNA template
DNA provides a template for making RNA sequence
II. Translation synthesis of polypeptide under directions from mRNA
translates mRNA sequence to amino acid sequence of polypeptide
happens at ribosomes
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Why is RNA used instead of just DNA?
provides protection for DNA and genetic information (original copy is left untouched)
more copies of protein can be made at the same time
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Difference in prokaryote and eukaryote protein synthesis
prokayotes no nucleus so ribosomes are near DNA, can happen faster
eukaryotes have nucleus so info from DNA is modified first, then has to get out of nucleus to ribosomes outside nucleus; happens slower
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Difference between prokaryote and eukaryote protein synthesis
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How do the nucleotides from DNA get read?
triplet codes = three consecutive bases64 possible code words specify 20 amino
acidsEx. AGU codes for serine
in DNA only one strand codes for proteins = template strand (each strand may act as a template for certain genes)
for a given gene the same strand is used all of the time
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RNA strand is complementary to DNA using the base pairing rules
C GA U (uracil)mRNA is synthesized in antiparallel direction
Ex. 3'ACC5' of DNA is template for 5'UGG3'
UGG = codon (triplet of mRNA)(can also mean triplet on nontemplate DNA strand, aka coding strand)
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The triplet code
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The dictionary of genetic code
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AUG start code and methionineall synthesized polypeptide strands start with methionine, but then an enzyme may break off methionine
stop codes: UAA, UGA, UAG
Ex. 5'AUGCAAGCUUAA3'
methionineglycinealanine stop
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Genetic code is universal
in all organisms tested AUG always means the same thing
genes can be transcripted and translated even if they are transplanted in other organisms
some exceptions: in some prokaryotes stop codon can be translated into an amino acidin some unicellular eukaryotes, may have slight variations of genetic code, not the norm
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How is DNA transcribed?1. RNA polymerase binds to a promoter on
the DNA strandtranscription unit = stretch of DNA that is transcribed into RNA
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2. RNA polymerase separates DNA strands and hooks together the RNA nucleotidesassemble in 5' to 3' directiondo not need a primerin prokaryotes have terminator signals end of
transcriptiondownstream = direction of transcriptionupstream = opposite direction of transcription
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Is this prokaryotic or eukayotic transcription?How can you tell?
Initiation RNA polymerase binds to promoter, DNA strands unwind, RNA synthesis starts
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Elongation:RNA polymerase moves downstream, elongating in 5' to 3' direction, behind DNA reforms double helix
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Bacteria have one RNA polymerase to synthesize mRNA and other types of RNA (ex. ribosomal RNA)
eukaryotes have three types of RNA polymerase: I,II,III
one used for mRNA synthesis is RNA polymerase IIothers transcribe RNA molecules not translated into protein
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3. Promoter determines which strand is being used as a templatein prokaryotes RNA polymerase attaches directly to promoterin eukaryotes, proteins called transcription factors help RNA polymerase bind to the promoter to start transcription
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Initiation of transcription at eukaryotic promoter
transcription initiation complex = transcription factors + RNA polymerase + promoter
part of promoter contains a TATA box
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4. RNA polymerase continues to untwist DNA as it moves downstream10 20 bases are paired with RNA at a timeadds bases to 3' endnew RNA comes away from DNA templateDNA double helix reformstranscribes 60 nucleotides per second
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5. one gene can be transcribed by many RNA polymerases, one after the other so many of the same proteins can be made
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6. Termination in prokaryotes terminator sequence where polymerase detaches
eukaryotes premRNA is cleaved while RNA polymerase II continues to transcribe DNA, have a polyadenylation signal sequence, (AAUAAA),then 1035 nucleotides downstream, RNA transcript is cut free
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RNA processing in Eukaryotes
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7. premRNA is then modified to mRNA
Added: 5'cap modified guanine (first 2040 bases)3' end polyA tail formed (added 50250 adenine nucleotides)
functions of botha. help mature mRNA out of nucleusb. help protect mRNA from hydrolytic enzymesc. once in cytoplasm, both help ribosomes attach to 5' end
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RNA processing addition of 5' cap and polyA tail
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8. RNA splicingare noncoding sections between the coding sections in the pre
mRNA that have to be removed noncoding or intervening sequences are called intronsexons = coding regions that are eventually expressed as amino
acids (exons "exit" the nucleus and to be translated)
introns have short nucleotide sequences before and after them called snRNP's small nuclear ribonucleoproteins (150 nucleotides long) = signal for RNA splicing
RNA in snRNP is called small nuclear RNA(snRNA) recognize splice sites
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snRNP's and other proteins make a spliceosome(cuts intron out and binds exons)
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The roles of snRNP's and splicesosome in RNA splicing
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In some organisms RNA splicing can occur with out spliceosome, occurs using ribozymes (RNA molecules that act as enzymes)
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Why are introns and RNA splicing important?can control gene activityhelps RNA get out of nucleus
some genes code for two different proteins depending on what exons remain (alternative RNA splicing)produces greater # of proteins made than # of genes
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Correspondance between exons and protein domains
domain = structural and functional region of a protein
ex. active site
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Translationcell interprets mRNA and builds polypeptide
gets interpreted by tRNA (transfer RNA)transfers amino acids to ribosome where they are joined together to make a polypeptideeach tRNA translates a specific mRNAanticodon region of tRNA is complementary to mRNA codon
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Basic concept of translation
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tRNA = RNA strand 80 nucleotides longhas 3D structure
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How tRNA is specific for amino acid
1. AminoacyltRNA synthetase (20) joins amino acid to tRNA
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2. correct match between tRNA and mRNAonly 45 tRNAscan pair with more than one mRNAdue to relaxed of base pairing rulesU at 5' end of anticodon can pair with A or G in third position = wobble
explains how codons can differ in 3rd base, not 1st or 2nd look at chart
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Ribosome = two subunits (large and small)
made of proteins and RNA molecules (rRNA)made in nucleolus of eukaryoteslarge and small subunits only join together when attach to mRNA molecule
*streptomycin and tetracycline are drugs that affect prokaryotes by inactivating ribosomes
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have a binding site for mRNA and three binding sites for tRNA
Psite = holds tRNA and the growing polypeptide chainA site = holds tRNA carrying the next
amino acid for the chainE site = exit site, where tRNAs leave the ribosome
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Ribosome
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Steps in translation initiation
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elongation
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termination
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several ribosomes can translate the message from one mRNA at the same time (called polyribosomes or polysomes)
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after production of polypeptide, protein gets folded into 3D structure and post translational modifications happen
some amino acids may be chemically modified ex. add sugar or phosphate group
enzymes may remove one or more amino acids from end of chain
protein could get cut in two pieces (ie.insulin)two separate chains may come together
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free ribosomes in cytosol make proteins that dissolve and function there
bound ribosomes to ER or nuclear envelopemakes proteins of endomembrane system and ones secreted from cell
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ribosomes switch from free to boundsignal peptides in the polypeptide chain will signal the ribosome to attach to the ER
signal recognized by signal recognition particle
other signal proteins can be used to attach to mitochondria, chloroplasts, etc.
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signal mechanism for targeting proteins to the ER
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Review of RNA types
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prokaryotic and eukaryotic differences
RNA polymerases are differenteukaryotes depend on transcription factors
transcription is terminated differentlyribosomes are differentprokaryotes simultaneously transcribe and translateeukaryotes transcription is segregated from translationeukaryotes use signals to target proteins to the proper cell organelle
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Coupled transcription and translation in bacteria
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Mutations allow cells to code for many of the proteins synthesizedMutationchanges in genetic material of a cell or viruspoint mutations involve one base pair of a gene
if it has adverse effect on offspring = disorderex. sickle cell anemia
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Sickle Cell Anemia
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Types of point mutations1. Base pair Substitutions =replacement of one nucleotide and its partner with another pair of nucleotides
a. silent mutation if it doesn't change the amino acidsome base pair mutations alter the protein being made can be troublesome
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b. missense mutations altered codon still codes for an amino acid and makes sense, but not right sense
c. nonsense mutation a point mutation that changes a codon into a stop codon
translation gets stopped earlyshorter than normal polypeptideprotein is nonfunctional
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Point Mutations
base pair substitutions
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2. insertions and deletionsaddtions or losses of nucleotide pairsalters reading frame (frameshift mutation)produce nonfunctional proteins
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Point Mutations
Base pair insertion and deletion
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MutagensSpontaneous mutations = mutations that happen during DNA replication, repair or recombination that lead to basepair substitutions, insertions or deletions
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mutagens = physical or chemical agents that change DNA to cause mutations
ex. xrays,UV light, chemicals
scientists have come up with tests to test chemicals for potential carcinogenic properties(Ames test)
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Revamp of gene definition:
A gene is a region of DNA whose final product is either a polypeptide or an RNA molecule
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Summary of transcription and translation
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