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Transcript of DNA
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DNA
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DNA
• must carry information• must be replicatable (inheritance)• must be changeable (mutation)
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DNA
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DNA structure
deoxyribonucleic acid - two directional polynucleotide strands in a double helix
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A brief digression for terminology:
O
C
CC
C4 1
23
Carbon moleculesin rings are numbered….
C5
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two directional polynucleotide strands in double helix
start with a ribosesugar…
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two directional polynucleotide strands in double helix
start with a ribosesugar…
remove an oxygen atcarbon 2’….
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two directional polynucleotide strands in double helix
start with a ribosesugar…
remove an oxygen atcarbon 2’…. add a phosphate group at 5’ side
add a nitrogenous base at 1’ side= a nucleotide
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two directional polynucleotide strands in double helix
A nucleotide, or base
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Bases = purines (adenine, guanine) and pyrimidines (cytosine, thymine)
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5’ end
3’ end
nucleotides are linked in chains with a phosphodiester bondfree ends of chain will have 5’ phosphate at one end,
3’ hydroxyl at the other end
two directional polynucleotide strands in double helix
phosphodiesterbond
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5’ end
3’ end
nucleotides are linked in chains with a phosphodiester bondfree ends of chain will have 5’ phosphate at one end,
3’ hydroxyl at the other end
two directional polynucleotide strands in double helix
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two directional polynucleotide strands in double helixHydrogen bonds
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Two strands pair up, nucleotides linked with hydrogen bondsadenosine pairs with thyminecytosine pairs with guanine
two directional polynucleotide strands in double helix
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Two strands pair up, nucleotides linked with hydrogen bondsadenosine pairs with thyminecytosine pairs with guanine
- abbreviated as “base pairs”
two directional polynucleotide strands in double helix
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two directional polynucleotide strands in double helix
Strands have polarity - 5'-hydroxyl group of first nucleotide at one end, 3'-hydroxyl group at other end (5’ to 3’ strand)
Strands run antiparallel: (5' -> 3') ATGGAATTCTCGCTC (3' <- 5') TACCTTAAGAGCGAG
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DNA replication: two strands are both available as templates for new strand result is doubling (2 complete new double helices)
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DNA replication: is semiconservative always occurs in 5’ to 3’ direction
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DNA replication: occurs at multiple replication forks (bubbles) along the DNA strand
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Important:
there are several DNA polymerases involved in replication DNA polymerases have a proof-reading and editing function
(exonuclease activity)
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TRANSCRIPTION
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Consider:
if all DNA was actively used:- most mutations would be lethal- there would be no ‘raw material’ for evolutionary change- what would happen to genes de-activated by mutation?
In fact, many errors and duplications leave ‘extra’ DNA
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Consider:
If there is excess DNA, it may be- only between genes- also interspersed within genes
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Consider:
If there is excess DNA, it may be- only between genes- also interspersed within genes
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Consider:
Not all gene products are required simultaneously; needs for proteins change or differ
- during development (e.g., milk digesting enzymes)- over time (e.g., digestive enzymes)- among organs (e.g., liver enzymes not used in muscle)- in response to stimuli (e.g., melanin, adrenalin)
therefore regulation of gene activity is needed
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Transcription:
Uses RNA as an intermediary - to assemble genes - to transmit the right information when/where it is needed
(regulation)
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Transcription:
Uses RNA as an intermediary - to assemble genes - to transmit the right information when/where it is needed
(regulation)
RNA is ribonucleic acid- has uracil instead of thymine- sugar is ribose instead of deoxyribose
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There are three types of RNA:
mRNA: messenger RNA – carries the code for a gene
rRNA: ribosomal RNA – used to construct ribosomes
tRNA: transfer RNA – short adapters to carry amino acid and its anti-codon
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DNA strand (double, helical) - permanent(5' -> 3') ATGGAATTCTCGCTC (coding, sense strand)
(3' <- 5') TACCTTAAGAGCGAG (template, antisense strand)
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DNA strand (double, helical) - permanent(5' -> 3') ATGGAATTCTCGCTC (coding, sense strand)
(3' <- 5') TACCTTAAGAGCGAG (template, antisense strand)
mRNA strand (single, linear) – temporary, as needed(5' -> 3') AUGGAAUUCUCGCUC (from template strand)
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DNA strand (double, helical) - permanent(5' -> 3') ATGGAATTCTCGCTC (coding, sense strand)
(3' <- 5') TACCTTAAGAGCGAG (template, antisense strand)
mRNA strand (single, linear) – temporary, as needed(5' -> 3') AUGGAAUUCUCGCUC (from template strand)
note: by taking information from the template (antisense) strand
of DNA, mRNA becomes the coding sequence
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DNA strand (double, helical) - permanent(5' -> 3') ATGGAATTCTCGCTC (coding, sense strand)
(3' <- 5') TACCTTAAGAGCGAG (template, antisense strand)
mRNA strand (single, linear) – temporary, as needed(5' -> 3') AUGGAAUUCUCGCUC (from template strand)
protein sequence (single, with 1, 2, 3, 4 structure) Met-Glu-Phe-Ser-Leu...
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promoter region: immediately upstream (5’ end) of its gene
Gene structure
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Steps in transcription:
1. initiation RNA polymerase recognizes and binds to promoter sequence - these contain TATAAA and TTGACA or CCAAT codes
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Steps in transcription:
1. initiation RNA polymerase recognizes and binds to promoter sequence - these contain TATAAA and TTGACA or CCAAT codes
2. elongation - similar to DNA replication - only one strand (template) is used
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Steps in transcription:
1. initiation RNA polymerase recognizes and binds to promoter sequence - these contain TATAAA and TTGACA or CCAAT codes 2. elongation - similar to DNA replication - only one strand (template) is used
3. termination - transcription keeps going for 1000-2000 bases beyond
end of ‘gene’
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After transcription: RNA processing
capping polyadenylation intron removal
UTR= untranslated region
promoter elements
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TRANSLATION:
The Genetic Code
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The genetic code
DNA and RNA have 4 types of basesproteins are composed of amino acids, of which there are 20
- so how do 4 bases encode 20 amino acids?
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The genetic code
“words” with a single base allow no combinations (4 words)
“words” with two bases allow 16 combinations (42)
“words” with three bases allow 64 combinations (43)= more than enough combinations for 20 amino acids
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The genetic code
• composed of nucleotide triplets (codons)
mRNA AUG GAA UUC UCG CUC
protein sequence Met Glu Phe Ser Leu
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The genetic code
• composed of nucleotide triplets (codons)• non-overlapping
mRNA AUG GAA UUC UCG CUC
protein sequence Met Glu Phe Ser Leu
NOT AUGGAAUUCUCGCUC
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The genetic code
• composed of nucleotide triplets (codons)• non-overlapping• unambiguous – each codon only specifies one amino acid• degenerate – most amino acids specified by several codons
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firs
t pos
itio
n
second position
third position
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Reading frame must be uniquely specified:
theredfoxatethehotdog
t her edf oxa tet heh otd og
th ere dfo xat eth eho tdo g
the red fox ate the hot dog
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start codon
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Reading frame must be uniquely specified:
mRNA code begins with start codon (AUG)
protein is constructed along open reading frame
translation stops at stop codon (UAA, UAG, or UGA)(only in frame: sequence out of frame does not work)
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Reading frame must be uniquely specified:
mRNA code begins with start codon (AUG)
protein is constructed along open reading frame
translation stops at stop codon (UAA, UAG, or UGA)(only in frame: sequence out of frame does not work)
GUCCCGUGAUGCCGAGUUGGAGUAAGUAACCU met pro ser trp ser lys stop
5’ 3’
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The genetic code
• composed of nucleotide triplets (codons)
• non-overlapping
• unambiguous
• degenerate
• nearly universal – except for portions of mitochondrial
DNA and a few procaryotes
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TRANSLATION:
assembling proteins
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Three types of RNA:
mRNA: messenger RNA – carries the code for a gene
GUCCCGUGAUGCCGAGUUGGAGUAGAUAACCU5’ 3’
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Three types of RNA:
mRNA: messenger RNA – carries the code for a generRNA: ribosomal RNA – used to construct ribosomes
- four types, used to make two-unit ribsome
(30 S)
(60 S)
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Three types of RNA:
mRNA: messenger RNA – carries the code for a generRNA: ribosomal RNA – used to construct ribosomestRNA: transfer RNA – short adapters to carry amino acid and its anti-codon
anticodon
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Steps in translation:
1. initiation ribosomal subunits recognize, bind to 5’ cap on mRNA initiator tRNA (with UAC anticodon) binds to AUG start codon
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Steps in translation:
1. initiation2. elongation next tRNA pairs with its codon peptidyl transferase
1. catalyzes formation of peptide bond between amino acids
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Steps in translation:
1. initiation2. elongation next tRNA pairs with its codon peptidyl transferase
1. catalyzes formation of peptide bond between amino acids2. breaks amino acid bond with previous tRNA
ribosome shifts over one codon
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Steps in translation:
1. initiation2. elongation3. termination stop codon is recognized, bound to by release factor, polypeptide
is freed
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Protein structureprimary: amino acid sequencesecondary: helix or pleated sheet, held with hydrogen bondstertiary: collapsed molecule with internal bondsquaternary: protein subunits combine to form functional protein
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Protein structure
quaternary: protein subunits combine to form functional protein
subunits may be from same gene, or differentmay need two (dimers), three (trimers), or more
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Protein function
enzymes – catalyze chemical reactions; most common proteinsusually have active sites (tertiary structure) that mediate function
structural proteinscollagen, keratin
transportershemoglobin
contractile – tissue and muscle movementactin, myosin
intercellular communicationinsulin, other hormones
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Fig. 9-20