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The Nature of Genes

Early ideas to explain how genes work came from studying human diseases.
Archibald Garrod proposed that patients with the disease alkapt­onuria lacked a particular enzyme.
Beadle and Tatum studied Neurospora crassa.
They looked for fungal cells lacking specific enzymes.
Beadle and Tatum results was that each mutated enzyme disrupted one key enzyme in the metabolic pathway.

Prokar­yotic Transc­ription

Prokar­yotic Transc­rip­tion: Single RNA polymerase
- Initiation of mRNA synthesis does not require a primer
Prokar­yotic Transc­ription requires a Promoter, Start Site, and a termin­ation site.
Transc­ription occurs in three major stages:
- Initiation
- Elongation
- Termin­ation
Initia­tion: RNA polymerase binds to the promoter
Promoter: Forms a recogn­ition and binding site for the RNA polyme­rase.
- Found upstream of the start site.
- Not transc­ribed.
- Asymet­rical: indicate site of initiation and direction of termin­ation.
Elonga­tion: RNA transcript grows in the 5'-to-3' direction as ribonu­cle­otides are added.
- Transc­ription bubble: contains RNA polyme­rase, DNA template, and growing RNA transc­ript.
- After the transc­ription bubble passes, the now-tr­ans­cribed DNA is rewound as it leaves the bubble.
Termin­ation: Marked by sequence that signals "stop" to polyme­rase.
- Causes the formation of phosph­odi­ester bonds to cease.
- RNA-DNA hybrid within the transc­ription bubble dissoc­iates.
- RNA polymerase releases the DNA.
- DNA rewinds.
Hairpin in RNA causes RNA polymerase to pause
U:A base pairs weaken the DNA/RNA bonding.
Prokar­yotic transc­ription is coupled to transl­ation
- mRNA begins to be translated before transc­ription is finished.

Frameshift mutations


- Addition or deletion of a single base
- Much more profound conseq­uences
- Alter reading frame downstream
- Triplet repeat expansion mutation
Hunting disease
Repeat unit is expanded in the disease allele relative to the normal
 

Transc­ription and Transl­ation

The Central Dogma
Inform­ation only flows from: DNA-->­RNA­-->­protein
First described by Francis Crick.
Transc­ription
DNA--> RNA
- DNA-di­rected synthesis of RNA
- Only template strand of DNA used
- T in DNA replaced by U in RNA.
- mRNA used to direct synthesis of polype­ptides.
Transl­ation
- Synthesis of polype­ptides.
- Takes place at ribosome.
- Requires several kinds of RNA.
RNA
All synthe­sized from DNA template by transc­ription
- Messenger RNA (mRNA).
- Ribosomal RNA (rRNA).
- Transfer RNA (tRNA).
- Small nuclear RNA (snRNA)
- Signal recogn­ition particle RNA (SRP RNA).
- Micro-RNA (miRNA).

Eukaryotic Transc­ription

3 different RNA polyme­rase!!
RNA polymerase I: Transc­ribes rRNA.
RNA polymerase II: treans­cribes mRNA and some snRNA.
RNA polymerase III: transc­ribes tRNA and some other small RNAs
Each RNA polymerase recognizes it own promoter.
Initiation of transc­rip­tion: Requires a series of transc­rption factors (helper).
- Transc­ription factors: Necessary to get the RNA polymerase II enzyme to a promoter* and to initiate gene expres­sion.
Elonga­tion: RNA transc­ribed from the DNA template.
Termin­ation not as well defined.
Initiation of trancr­iption
- Transc­ription factors bind to a promoter region and recruit RNA polyme­rase.
- Forms the initation complex.

Protein Targeting

In eukary­otes, transl­ation may occur in the cytoplasm or the rough endopl­asmic reticulum (RER).
Signal sequences at the beginning of the polype­ptide sequence bind to the signal recogn­ition (SRP).

- The signal sequence and SRP are recognized by RER receptor proteins
- Docking holds ribosome to RER
- Beginning of the protei­n-t­raf­ficking pathway

Mutation: Altered Genes

Point mutations
alter a single base
Base substi­tution
substitute one base for another
Siletn mutation
same amino acid inserted
Missense mutation
changes amino acid inserted
- Transi­tions
- Transv­ersions
Nonsense mutations
changed to stop codon
 

The Genetic Code

Francis Crick and Sydney Brenner determined how the order of nucleo­tides in DNA encoded amino acid order.
- They introduced single nucleotide insertions or deletions and looked for mutations (Frameshift mutations)
A Codon is a block of three DNA nucleo­tides corres­ponding to an amino acid,
Spaced Codons: Codon sequence in a gene punctu­ated.
Unspaced Codons: codons adjacent to each other.
- Marshall Nirenberg identified the codons that specify each amino acid.
Stop Codon: 3 codons (UAA, UGA, UAG) used to terminate transl­ation
Start Codon: Codon (AUG) used to signify the start of transl­ation
Code is degene­rate: Some amino acids are specified by more that one codon.
Code practi­cally unicersal: Strongest evidence that all living things share common ancestry.
- Advanced in genetic engine­ering.
- Mitoch­ondria and cloroplast have some differ­ences in "­sto­p" signals.

mRNA modifi­cations

In eukaryotes the primary transcript must be modified to become mature mRNA
Addition of a 5' cap Protects nucleo­tides from getting lost, from degrad­ation.
- Involved in transl­ation initia­tion.
Addition of a 3' poly-A tail Created by poly-A polyme­rase, protection from degrad­ation
- Puts whole string of A's (AAA) to protect!
Removal of noncoding sequences (introns): Pre-mRNA splicing done by splice­osome.
- Cut it out to get rid of it!!!

tRNA charging reaction

Each aminoa­cyl­-tRNA synthetase recognizes only 1 amino acid but several tRNAs.
Charged tRNA has an amino acid added using the energy from ATP.
-Can undergo peptide bond formation without additional energy.
Ribosomes do not verify amino acid attached to tRNA.
The ribosome has multiple tRNA binding sites:
P site: binds the tRNA attached to the growing peptide chain
A site: binds the tRNA carrying the next amino acid.
E site: binds the tRNA that carried the last amino acid, tRNA exits ribosome.
The ribosome has two primary functions
- Decode the mRNA.
- Form peptide bonds.
Peptidyl transf­erase:
- Enzymatic component of the ribosome.
- Forms peptide bonds between amino acids.

Chromo­somal mutations

Chang the structure of a chromosome
Deletions: part of chromosome is lost
Duplic­ation: part of chromosome is copied
Inversion: part of chromosome in reverse order
Transl­oca­tion: part of chromosome is moved to a new location
 

Eukaryotic pre-mRNA splicing

Introns
non-coding sequences
Exons
sequences that will be translated
Small ribonu­cle­opr­otein particles (snRNPs "­snu­rps­")
Looks for introns and exons and recognizes it.
Splice­osomes
respon­sible for removing introns
snRNPs cluster with other proteins to form splice­osome

tRNA and Ribosomes

tRNA moleules carry amino acids to the ribosome for incorp­oration into a polype­ptide.
- Aminoa­cyl­-tRNA synthetase add amino acids to the acceptor stem of tRNA.
- Anticodon loop contains 3 nucleo­tides comple­mentary to mRNA codons.

Transl­ation

Process by which the mRNA transcript is read by the ribosomes and used to make a polype­ptide.
Occurs in 3 main stages:
- Initiation
- Elongation
- Termin­ation
There are some important differ­ences between transl­ation in prokar­yotes and eukary­otes.
In prokar­yotes, initiation complex includes Initiator tRNA charged with N-form­ylm­eth­ionine {[nl}}- Small ribosomal subunit
- mRNA strand

- Ribosome binding sequence (RBS) of mRNA positions small subunit correctly.
- Large subunit now added.
- Initiator tRNA bound to P site with A site empty.
Initia­tions in eukaryotes similar except:
- Initiating amino acid is methio­nine.
- Lack of an RBS – small subunit binds to 5′ cap of mRNA.
Elongation adds amino acids
- 2nd charged tRNA can bind to empty A site
- Requires elongation factor called EF-Tu to bind to tRNA and GTP
- Peptide bond can then form.
- Addition of successive amino acids occurs as a cycle.

- There are fewer tRNAs than codons
- Wobble pairing allows less stringent pairing between the 3′ base of the codon and the 5′ base of the anticodon
- This allows fewer tRNAs to accomm­odate all codons
Termin­ation
- Elongation continues until the ribosome encounters a stop codon
- Stop codons are recognized by release factors which release the polype­ptide from the ribosome
       
 

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