Gene Expression and Protein Synthesis

Speeds up the transcription process by binding to DNA sequences that may be located several thousands nucleotides away from the transcription site. These sequences are called enhancers

2nd type of transcription Factor

-Involes a type of enhancer called response elements • These are activated in response to an outside stimulus • The stimulus maybe heat shock, heavy metal toxicity, or hormonal signal

3rd type of transcription factor

Second Genetic Code

A code used in order for an enzyme to specifically recognize its proper tRNA and amino acid (ie. Aminoacyl-tRNA Synthetase). Once AA is in tRNA you can not remove it. In Other words the anticodon of the tRNA will match the codon of mRNA

Elongation

A process in which RNA polymerase zips up the complementary bases by forming a phosphate ester bond between each ribose and the next phosphate group

ADA adenosine deaminase

A successful form of gene therapy that involves an enzyme in purine catabolism

Phosphorylated protein kinase

A type of enzyme that enters the nucleus where it phosphorylates transcription factors which Aid in the transcription Cascade. It is a type of signal that helps speed up transcription, originates from outside the cell

• Amino acid activated by reacting with a molecule of ATP • The AA is the bound to its own tRNA molecule with the aid of an enzyme (a synthetase) like (aminoacyl-tRNA synthetases) specific to that AA and that tRNA molecule

Activation Steps

Mutation

An error in the copying of a sequence of bases

Enhancer

Another type of control element, a DNA sequence that can be far removed from the promoter region. They also bind to transcription factors

No, only some can cause cancer when introduced into the body. Although most carcinogens are mutagens, the reverse is not true.

Are all mutagens also carcinogens?

Enhancers

Brought closely to promoters by the formation of a loop ATF binds to the enhancer element and forms of bridge this complex than allows the RNA polymerase II to speed up the transcription when the higher-than-normal production of proteins is needed

Yes, it can result in an inborn genetic disease carried as a "recessive gene" from generation to generation with no individual demonstrating the symptoms of the disease. When both parents carry recessive mutations an offspring has 25% chance. If dominant everyone will show symptoms

Can a harmful mutation-causing genetic disease exist from generation to generation without exhibiting the symptoms of the disease? Explain

The Genetic Code

Each amino acid in the protein language has a corresponding WORD in the RNA language. Each word in the RNA language is a sequence of three bases. This correspondence between three bases and one Amino acid is called____

1 Binding to the A site- takes place with the aid of proteins called elongation factors and GTP 2. Forming the first Peptide- At the a site the new AA, is linked to fMet in a peptide bonds by the enzyme peptidyl transferase • The empty tRNA remains on the P site 3. Translocation- the whole ribosome moves one codon along the mRNA. The dipeptide is translocated from A site to the P site. • the empty tRNA is moved to the E site 4. Forming the Second Peptide- After the translocation, the A site is associated with the next codon on the mRNA. Remember anticodon of tRNA and codon of mRNA only

Elongation has 4 steps, list them:

6 TFs must bind to the DNA and RNA polymerase to initiate transcription 1. They form the pre-initiation complex 2. In order for transcription to occur there needs to be a conversion to the "open complex", which involves the phosphorylation of the C-terminal end of the RNA polymerase

Events of Pol II transcription

The formyl group does not remain in the finished protein, so it is cleaved off by a specific protein. Methionine- is not found at the N-terminus if proteins. It is also cleaved off so the correct AA is at the N-terminus

Explain what happens to the fMet initially put at the N-terminus?

Anticodon

Group of three bases on a tRNA molecule that are complementary to an mRNA codon. Also know as codon recognition site.

Linked together by the usual phosphodiester bonds between the ribose residues

How are the adenine nucleotides linked together in the poly-A-tails?

by NER Nucleotide excision repair, which can prevent mutations by cutting out damaged areas and recent the sizing them

How do cells repair mutations caused by x-rays?

Enzymes that recognize specific sequences on DNA and catalyze the hydrolysis of phosphodiester bonds in that region thereby cleaving both strands of the DNA

How do restriction endonucleases operate?

It can lead to different proteins when the final mRNA is translated. There's a diversity caused by the different ways of modifying the proteins after they are translated

How does alternative splicing lead to protein diversity?

6 , all named TFII and then letter

How many GTFs are needed for the transcription of genes that will lead to mRNA (Pol II transcription)

• RNA Polymerase- Pol I • Pol II- Catalyzes mRNA formation • Pol III- Catalyzes tRNA formation as well as ONE Ribosomal subunit and others like snRNA

In eukaryotes there are three kinds of polymerases that catalyze transcription

Nucleus

In what part of the eukaryote cell does transcription occur?

1. Forming the pre-initiation complex-tRNA(fMet) methionine residue is used, but only for initiation. Attached to 30S Ribosomal body along with GTP forms complex. Use of proteins called initiation factors 2. Migration to mRNA- Pre-initiation complex binds to mRNA. The Ribosome is aligned on mRNA by recognizing Shine-Dalgarno sequence which is complementary do the sequence on the 30S ribosomal unit. The anticodon of the fMet-tRNA , UAC lines up against the start codon, AUG. 3. Forming the full Ribosomal complex- The 50S ribosomal body joins the 30s Ribosomal complex.

Initiation Steps

• Promoters • Enhancers • Response elements

List the three entities that regulate transcription in Eukaryotes

UAA, UAG and UGA

List three stop signs that terminate protien synthesis

Promoters

Located near transcription site, defined by an initiator, like a TATA box or copies of other sequences like GGGCGG called GC box

Silencers

Opposite of enhancer; they slow down transcription

Mutagens

Organic compounds that can induce mutations by reacting with DNA

a) Removal of methionine- removed from the N terminus by an enzyme, methionine aminopeptidase cleaves the peptide bond b) Chaperoning- Chaperones (proteins) help newly synthesized polypeptide chains to fold properly c) Degradation of misfolded proteins- by proteasomes

Post-translational controls

General Transcription Factor (GTF)

Proteins that form a complex with RNA polymerase and the DNA and help to position the RNA polymerase correctly and stimulate the initiation of transcription

The central Dogma of molecular biology

States that the information contained in DNA molecules is transferred to RNA molecules, and then from RNA molecules the information is expressed in the structure of proteins

After final translocation, the next codon reads "stop" or UAA UGA or UAG. No more AAs can be added • Releasing factors leave the polypeptide chain from the last tRNA via a GTP mechanism. • At the end the whole mRNA is released from the ribosome

Termination

Gene Regulation

The Control process by which the expression of a gene is turned on or off

Structural gene: it is transcribed into RNA Regulatory gene: controls the transcription

The Eukaryotic Gene has two major parts: name them.

Gene Expression

The activation of a gene to produce a specific protein it involves both transcription and translation

Gene therapy

The alteration of the genes of a person afflicted with a genetic disease

Translation

The process in which information encoded in an mRNA molecule is used to assemble a specific protein

• P site- where he growing peptide chain will bind the one next to it is • A (acceptor) site- It accepts the incoming tRNA bringing the next amino acid as the full initiation complex is completed the initiation factors (proteins) dissociate and the GTP is hydrolyzed to GDP

There are three sites on the ribosome, each participating in the translation. Identify them and describe what is happening at each site

The process in which information encoded in a DNA molecule is copied into an mRNA molecule

Transcription

DNA->RNA

Transcriptional level regulations are

tRNA. message goes from language of nucleotides into the language of amino acids

Translation is done by which type of RNA?

mRNA->protein

Translational level regulations operate from

Codons

Triplets of bases on mRNA are called

The smaller body first then the larger one joins afterwards. ie. 40S then 60S in Eukaryotes

What Ribosomal body is mRNA attached to in translation?

Enhancers are regulatory regions on the DNA that may be thousands of nucleotides away from the transcription site. They may be brought into the vicinity of transcription by forming Loops. When these Loops form, the rate of transcription is modified

What are Enhancers? How do they work?

Are formed by the action of some restriction endonucleases, they are called sticky ends because they can combine together with hydrogen bondingDyfuh ioj

What are sticky ends?

Larger body: 60S ribosome Smaller body: 40S Ribosome "S" stands for Svedburg (a measure of density in centrifugation) mRNA is attached to the smaller body and then later joined by the larger body

What are the Ribosomal subunits for eukaryotic translation?

1. The strand that serves as a template for the formation of RNA has several names • Template strand, (-) strand, antisense strand 2. The other strand not used as a template, actually has a sequence that much of the RNA that will be produced • Coding strand, sense strand

What are the different names used for the two strands of DNA involved in transcription?

Larger 50S Smaller 30S

What are the ribosomal subunits for prokaryotic translation?

1. Activation 2. Initiation 3. Elongation 4. Termination

What are the stages of protein Synthesis?

1. The sites to which enzymes attach the amino acids 2. Codon Recognition site Note: each tRNA is specific for one amino acid only

What are the two most important sites on tRNA molecules?

Ex vivo therapy- somatic cells removed from patient, altered with the gene therapy, and then return to the patient. In vivo therapy- Virus is to directly infect a patients tissues. The most common Vector for this delivery is the DNA virus adenovirus.

What are the two types of delivery methods In human gene therapy?

Binding proteins that interacts with all three RNA polymerases at their promoter regions

What are transcription factors?

• Is an initiation codon • The amino acid methionine, this means that in all protein synthesis the first amino acid initially put into the protein is always methionine, it can also be put in the middle of the chain

What is AUG? What amino acid does it code for?

The promotor sequence is a regulatory DNA sequence found upstream of the structural gene that contains the initiation signal for RNA transcription. Also contain consensus sequences.

What is a promoter sequence?

The portion of the structural gene that is retained after splicing, it enodes protein

What is an Exon?

A DNA sequence that is eventually spliced out of the RNA and not part of the final RNA product of transcription

What is an Intron?

A sequence of bases that helps the RNA polymerase identify where transcription should begin

What is the consensus sequence in transcription?

Both are DNA sequences that bind to transcription factors. Response elements may activate several genes when the organism is challenge metabolically by heavy metals, by heat, or by a reduction in oxygen pressure

What is the difference between an enhancer and a response element?

Catalyze the formation of most of the rRNA

What is the function of RNA polymerase?

Play a role in post-translational degradation of damage proteins. These damaged proteins are degraded by proteosomes

What is the function of proteosomes in quality control?

UGU, UGC

What is the genetic code for Cystine ?

Enzymes that start the unwinding of the DNA double helix PRIOR to transcription, they break down the hydrogen bonds between base

What is the role of helicase in transcription?

Metal-binding Transcription factors, which are proteins, interact with specific regions of DNA. The recognition comes by hydrogen bonding between a nucleotide in the DNA and the side chain of an amino acid in the protein

What kind of interactions exist between metal-binding fingers and DNA?

1. The specificity of a tRNA for its unique amino acid 2. Recognition of the stop codon 3. Post-translational controls

What mechanisms ensure quality control during translation?

A drug that inhibits the phosphatase would allow elongation but initiation would be halted, so that another round of transcription could not occur

What would happen to the transcription process if a drug added to a eukaryotic cell inhibited the phosphatase?

These are triplets base pairs located on the mRNA

Where are codons located?

The active site of the enzyme. Ensures that each amino acid is linked to its correct tRNA. The two sieving steps work on the basis of the size of the amino acid

Where are the sieving portions of AARS enzymes located? What is their function?

Cytoplasm

Where does most of the translation occur in a eukaryote cell?

On the DNA strand to be transcribed, there is a sequence of bases at the RNA polymerase recognizes as a place to start

Where is an initiation signal located?

In the nitrogen number 7 of guanine

Where is the methyl group located in the guanine cap?

At the 5' end of the template strand that is being transcribed, it can also be said to be at the 3' end of the coding strand

Which end of the DNA contains the termination signal?

molecules that bind to DNA include RNA polymerase transcription factors and other proteins that May bind the RNA polymerase and a transcription Facto

Which molecules are involved in gene regulation at the transcriptional level?