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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 Presentation
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Chapter 17From Gene to
Protein
Question?
How does DNA control a cell? By controlling Protein
Synthesis. Proteins are the link between
genotype and phenotype.
Central DogmaDNA
Transcription
RNA Translation
Polypeptide
Explanation
DNA - the Genetic code or genotype.
RNA - the message or instructions.
Polypeptide - the product for the phenotype.
DNA vs RNA
DNA RNASugar – deoxyribose riboseBases – ATGC AUGCBackbones – 2 1Size – very large smallUse – genetic code varied
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.
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).
Codon
A 3-nucleotide “word” in the Genetic Code.
64 possible codons known.
Codon Dictionary
Start- AUG (Met) Stop- UAA
UAG UGA
60 codons for the other 19 AAs.
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.
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.
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.
Transcription
Process of making RNA from a DNA template.
Transcription Steps
1. RNA Polymerase Binding
2. Initiation
3. Elongation
4. Termination
RNA Polymerase
Enzyme for building RNA from RNA nucleotides.
Binding
Requires that the enzyme find the “proper” place on the DNA to attach and start transcription.
Binding
Is a complicated process Uses Promoter Regions on
the DNA (upstream from the information for the protein)
Requires proteins called Transcription Factors.
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.
Transcription Factors
Proteins that bind to DNA before RNA Polymerase.
Recognizes TATA box, attaches, and “flags” the spot for RNA Polymerase.
Initiation
Actual unwinding of DNA to start RNA synthesis.
Requires Initiation Factors.
Elongation
RNA Polymerase untwists DNA 1 turn at a time and adds complimentary bases.
Exposes 10 DNA bases for pairing with RNA nucleotides.
Elongation
Enzyme moves 5’ 3’. Rate is about 60 nucleotides
per second.
Comment
Each gene can be read by sequential RNA Polymerases giving several copies of RNA.
Result - several copies of the protein can be made.
Termination
DNA sequence that tells RNA Polymerase to stop.
Ex: AATAAA RNA Polymerase detaches
from DNA after closing the helix.
Final Product
Pre-mRNA This is a “raw” RNA that will
need processing.
Modifications of RNA
1. 5’ Cap
2. Poly-A Tail
3. Splicing
5' Cap
Modified Guanine nucleotide added to the 5' end.
Protects mRNA from digestive enzymes.
Recognition sign for ribosome attachment.
Poly-A Tail
150-200 Adenine nucleotides added to the 3' tail
Protects mRNA from digestive enzymes.
Aids in mRNA transport from nucleus.
RNA Splicing
Removal of non-protein coding regions of RNA.
Coding regions are then spliced back together.
Introns
Intervening sequences. Removed from RNA. Some contain sequences that
regulate gene expression and many affect gene products
Exons
Expressed sequences of RNA.
Translated into AAs.
Introns - Function
Left-over DNA (?) Way to lengthen genetic
message to protect coding regions.
Old virus inserts (?)
Introns- Function
Way to create new proteins with exon shuffling
New combinations of exons= new proteins for evolution
Final RNA Transcript
Translation
Process by which a cell interprets a genetic message and builds a polypeptide.
Materials Required
tRNA Ribosomes mRNA
Transfer RNA = tRNA
Made by transcription. About 80 nucleotides long. Carries AA for polypeptide
synthesis.
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.
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.
Example
DNA - GAC mRNA - CUG tRNA anticodon - GAC
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.
Large subunit
Proteins
rRNA
Both sununits
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
Translation Steps
1. Initiation
2. Elongation
3. Termination
Initiation
Brings together: mRNA A tRNA carrying the 1st AA 2 subunits of the ribosome
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
Initiation
Requires other proteins called "Initiation Factors”.
GTP used as energy source.
Elongation Steps:
1. Codon Recognition
2. Peptide Bond Formation
3. Translocation
Codon Recognition
tRNA anticodon matched to mRNA codon in the A site.
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
After bond formation
The polypeptide is now transferred from the tRNA in the P-site to the tRNA in the A-site.
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.
Comment
Elongation takes 60 milliseconds for each AA added.
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.
Polyribosomes
Cluster of ribosomes all reading the same mRNA.
Another way to make multiple copies of a protein.
Comment
Polypeptide usually needs to be modified before it becomes functional.
Examples
Sugars, lipids, phosphate groups added.
Some AAs removed. Protein may be cleaved. Join polypeptides together
(Quaternary Structure).
End of Part 1
Mutations
Changes in the genetic makeup of a cell.
May be at chromosome (review chapter 15) or DNA level
DNA or Point Mutations
Changes in one or a few nucleotides in the genetic code.
Effects - none to fatal.
Types of Point Mutations
1. Base-Pair Substitutions
2. Insertions
3. Deletions
Base-Pair Substitution
The replacement of 1 pair of nucleotides by another pair.
Sickle Cell Anemia
Types of Substitutions
1. Missense - altered codons, still code for AAs but not the right ones
2. Nonsense - changed codon becomes a stop codon.
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.
Nonsense Effect
Stops protein synthesis. Leads to nonfunctional
proteins unless the mutation was near the very end of the polypeptide.
Sense Mutations
The changing of a stop codon to a reading codon.
Result - longer polypeptides which may not be functional.
Insertions & Deletions
The addition or loss of a base in the DNA.
Cause frame shifts and extensive missense, nonsense or sense mutations.
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.
Mutagenesis
Process of causing mutations or changes in the DNA.
Mutagens
Materials that cause DNA changes.
1. Radiationex: UV light, X-rays
2. Chemicalsex: 5-bromouracil
Spontaneous Mutations
Random errors during DNA replication.
Comment
Any material that can chemically bond to DNA, or is chemically similar to the nitrogen bases, will often be a very strong mutagen.
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
Protein vs RNA
Protein – usually structure or enzyme for phenotype
RNA – often a regulatory molecule which will be discussed in future chapters.