chapter 17 from gene to protein
DESCRIPTION
Chapter 17 From Gene to Protein. Question?. How does DNA control a cell? By controlling Protein Synthesis. Proteins are the link between genotype and phenotype. Central Dogma. DNA Transcription RNA Translation Polypeptide. Explanation. DNA - the Genetic code or genotype. - PowerPoint PPT PresentationTRANSCRIPT
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Chapter 17From Gene to
Protein
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Question?
How does DNA control a cell? By controlling Protein
Synthesis. Proteins are the link between
genotype and phenotype.
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Central DogmaDNA
Transcription
RNA Translation
Polypeptide
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Explanation
DNA - the Genetic code or genotype.
RNA - the message or instructions.
Polypeptide - the product for the phenotype.
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DNA vs RNA
DNA RNASugar – deoxyribose riboseBases – ATGC AUGCBackbones – 2 1Size – very large smallUse – genetic code varied
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Genetic Code
Sequence of DNA bases that describe which Amino Acid to place in what order in a polypeptide.
The genetic code gives the primary protein structure.
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Genetic Code
Is based on triplets of bases. Has redundancy; some AA's
have more than 1 code. Proof - make artificial RNA and
see what AAs are used in protein synthesis (early 1960’s).
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Codon
A 3-nucleotide “word” in the Genetic Code.
64 possible codons known.
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Codon Dictionary
Start- AUG (Met) Stop- UAA
UAG UGA
60 codons for the other 19 AAs.
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Code Redundancy
Wobble effect: Third base in a codon shows "wobble”.
First two bases are the most important in reading the code and giving the correct AA. The third base often doesn’t matter.
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Code Evolution
The genetic code is nearly universal.
Ex: CCG = proline (all life) Reason - The code must have
evolved very early. Life on earth must share a common ancestor.
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Reading Frame and Frame Shift
The “reading” of the code is every three bases (Reading Frame)
Ex: the red cat ate the rat Frame shift – improper groupings
of the bases Ex: thr edc ata tet her at The “words” only make sense if
“read” in this grouping of three.
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Transcription
Process of making RNA from a DNA template.
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Transcription Steps
1. RNA Polymerase Binding
2. Initiation
3. Elongation
4. Termination
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RNA Polymerase
Enzyme for building RNA from RNA nucleotides.
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Binding
Requires that the enzyme find the “proper” place on the DNA to attach and start transcription.
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Binding
Is a complicated process Uses Promoter Regions on
the DNA (upstream from the information for the protein)
Requires proteins called Transcription Factors.
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TATA Box
Short segment of T,A,T,A Located 25 nucleotides
upstream from the initiation site. Recognition site for
transcription factors to bind to the DNA.
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Transcription Factors
Proteins that bind to DNA before RNA Polymerase.
Recognizes TATA box, attaches, and “flags” the spot for RNA Polymerase.
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Initiation
Actual unwinding of DNA to start RNA synthesis.
Requires Initiation Factors.
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Elongation
RNA Polymerase untwists DNA 1 turn at a time and adds complimentary bases.
Exposes 10 DNA bases for pairing with RNA nucleotides.
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Elongation
Enzyme moves 5’ 3’. Rate is about 60 nucleotides
per second.
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Comment
Each gene can be read by sequential RNA Polymerases giving several copies of RNA.
Result - several copies of the protein can be made.
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Termination
DNA sequence that tells RNA Polymerase to stop.
Ex: AATAAA RNA Polymerase detaches
from DNA after closing the helix.
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Final Product
Pre-mRNA This is a “raw” RNA that will
need processing.
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Modifications of RNA
1. 5’ Cap
2. Poly-A Tail
3. Splicing
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5' Cap
Modified Guanine nucleotide added to the 5' end.
Protects mRNA from digestive enzymes.
Recognition sign for ribosome attachment.
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Poly-A Tail
150-200 Adenine nucleotides added to the 3' tail
Protects mRNA from digestive enzymes.
Aids in mRNA transport from nucleus.
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RNA Splicing
Removal of non-protein coding regions of RNA.
Coding regions are then spliced back together.
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Introns
Intervening sequences. Removed from RNA. Some contain sequences that
regulate gene expression and many affect gene products
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Exons
Expressed sequences of RNA.
Translated into AAs.
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Introns - Function
Left-over DNA (?) Way to lengthen genetic
message to protect coding regions.
Old virus inserts (?)
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Introns- Function
Way to create new proteins with exon shuffling
New combinations of exons= new proteins for evolution
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Final RNA Transcript
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Translation
Process by which a cell interprets a genetic message and builds a polypeptide.
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Materials Required
tRNA Ribosomes mRNA
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Transfer RNA = tRNA
Made by transcription. About 80 nucleotides long. Carries AA for polypeptide
synthesis.
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Structure of tRNAYou have a diagram of this
Has double stranded regions and 3 loops.
AA attachment site at the 3' end.
1 loop serves as the Anticodon.
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Anticodon
Region of tRNA that base pairs to mRNA codon.
Is a compliment to the mRNA bases, so reads the same as the DNA codon.
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Example
DNA - GAC mRNA - CUG tRNA anticodon - GAC
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Ribosomes
Two subunits made in the nucleolus.
Made of rRNA (60%)and protein (40%).
rRNA is the most abundant type of RNA in a cell.
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Large subunit
Proteins
rRNA
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Both sununits
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Large Subunit Has 3 sites for tRNA. P site: Peptidyl-tRNA site -
carries the growing polypeptide chain.
A site: Aminoacyl-tRNA site -holds the tRNA carrying the next AA to be added.
E site: Exit site
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Translation Steps
1. Initiation
2. Elongation
3. Termination
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Initiation
Brings together: mRNA A tRNA carrying the 1st AA 2 subunits of the ribosome
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Initiation Steps:
1. Small subunit binds to the mRNA.
2. Initiator tRNA (Met, AUG) binds to mRNA.
3. Large subunit binds to mRNA. Initiator tRNA is in the P-site
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Initiation
Requires other proteins called "Initiation Factors”.
GTP used as energy source.
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Elongation Steps:
1. Codon Recognition
2. Peptide Bond Formation
3. Translocation
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Codon Recognition
tRNA anticodon matched to mRNA codon in the A site.
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Peptide Bond Formation
A peptide bond is formed between the new AA and the polypeptide chain in the P-site.
Bond formation is by rRNA acting as a ribozyme
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After bond formation
The polypeptide is now transferred from the tRNA in the P-site to the tRNA in the A-site.
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Translocation tRNA in P-site is released. Ribosome advances 1 codon,
5’ 3’. tRNA in A-site is now in the P-
site. Process repeats with the next
codon.
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Comment
Elongation takes 60 milliseconds for each AA added.
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Termination
Triggered by stop codons. Release factor binds in the
A-site instead of a tRNA. H2O is added instead of AA,
freeing the polypeptide. Ribosome separates.
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Polyribosomes
Cluster of ribosomes all reading the same mRNA.
Another way to make multiple copies of a protein.
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Comment
Polypeptide usually needs to be modified before it becomes functional.
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Examples
Sugars, lipids, phosphate groups added.
Some AAs removed. Protein may be cleaved. Join polypeptides together
(Quaternary Structure).
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End of Part 1
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Mutations
Changes in the genetic makeup of a cell.
May be at chromosome (review chapter 15) or DNA level
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DNA or Point Mutations
Changes in one or a few nucleotides in the genetic code.
Effects - none to fatal.
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Types of Point Mutations
1. Base-Pair Substitutions
2. Insertions
3. Deletions
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Base-Pair Substitution
The replacement of 1 pair of nucleotides by another pair.
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Sickle Cell Anemia
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Types of Substitutions
1. Missense - altered codons, still code for AAs but not the right ones
2. Nonsense - changed codon becomes a stop codon.
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Missense Effect
Can be none to fatal depending on where the AA was in the protein.
Ex: if in an active site - major effect. If in another part of the enzyme - no effect.
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Nonsense Effect
Stops protein synthesis. Leads to nonfunctional
proteins unless the mutation was near the very end of the polypeptide.
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Sense Mutations
The changing of a stop codon to a reading codon.
Result - longer polypeptides which may not be functional.
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Insertions & Deletions
The addition or loss of a base in the DNA.
Cause frame shifts and extensive missense, nonsense or sense mutations.
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Question? Loss of 3 nucleotides is often
not a problem. Why? Because the loss of a 3 bases
or one codon restores the reading frame and the protein may still be able to function.
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Mutagenesis
Process of causing mutations or changes in the DNA.
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Mutagens
Materials that cause DNA changes.
1. Radiationex: UV light, X-rays
2. Chemicalsex: 5-bromouracil
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Spontaneous Mutations
Random errors during DNA replication.
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Comment
Any material that can chemically bond to DNA, or is chemically similar to the nitrogen bases, will often be a very strong mutagen.
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What is a gene?
A gene is a region of DNA that can be expressed to produce a final functional product.
The product can be a protein or a RNA molecule
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Protein vs RNA
Protein – usually structure or enzyme for phenotype
RNA – often a regulatory molecule which will be discussed in future chapters.