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Dr. Bruist - Molecular Biology - Exam III - Protein Synthesi
Exam III 2010
163
Chemistry
Undergraduate 4
04/26/2010

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Term
Anticodon in the anticodon loop reads what on what?
Definition
The codon on the mRNA.
Term
How does the Amino Acid attach to the tRNA?
Definition
It is esterified to the 3' end of the tRNA at Cytosine-cytosine-adenine end (or CCA stem).
Term
What are some commonalities between different tRNAs? Why?
Definition
They have all the exactly same structure because they need to fit into any ribosome the same way.
Term
What puts amino acids with their appropriate tRNA?
Definition
Aminoacyl-tRNA synthetases
Term
What is the name of the complex made by amino acids and their tRNA?
Definition
Aminoacyl-tRNA -> Covalent compound
Term
For each amino acid there is a unique...
Definition
Aminoacyl-tRNA synthetase to bind it to tRNA.
Term
Aminoacyl-tRNA synthetase uses...
Definition
ATP to make a high energy ester linkage between the amino acid and the tRNA.
Term
Ribosomes are usually...
Definition
70S.
Term
Large subunit is usually..
Definition
50s = 23s + 5s RNAs + 34 proteins
Term
Small subunit is usually...
Definition
30s = 16s RNA + 21 protiens.
Term
What are the three sites for tRNA?
Definition
APE sites
Term
What is the A site?
Definition
The A site is for the incoming aminoacyl-tRNA group.
Term
The P site of Ribosomes are for the...
Definition
Peptidyl site where the previous tRNA is attached to the growing peptide chain.
Term
The E site is for...
Definition
...exit site where the deacylated tRNAs leave.
Term
In what way are amino acids synthesized?
Definition
They are made amino to carboxylic end.
Term
mRNA is read by the ribosomes in what order?
Definition
5' to 3'
Term
Which part of the mRNA is translated?
Definition
The ORF (Open reading frame)
Term
How many ribosomes can bind to mRNA?
Definition
Many -- its hard to count.
Term
Can the ribosomes catch mistakes if the wrong amino acid is attached to the tRNA?
Definition
No.
Term
What is the initiator codon in prokaryotes? How is it recognized?
Definition
AUG. It is recognized by an initiator tRNA.
Term
In prokaryotes, the initiator sequence AUG is the first AUG after what?
Definition
The Shine-Delgarno sequence.
Term
What is the Shine-Delgarno sequence?
Definition
The Shine-Delgarno sequence is site where the ribosome binds onto the mRNA.
Term
The Shine-Delgarno sequence interacts with which part of the rRNA?
Definition
16s part of the small subunit of the RNA.
Term
In prokaryotes, the initiator tRNA carries what?
Definition
N-formylmthionine (fMet)
Term
In prokaryotes, there are a bunch of initiation factors which recruit...
Definition
...mRNA, small ribosomal subunit, and the initiator fMet-tRNA complex.
Term
The large subunit is added when?
Definition
After the addiction of the small subunit.
Term
After the addition of the large subunit, what gets added next?
Definition
fMet-init-tRNA is in the P site. The A and E sites are open.
Term
What type of hydrolysis is uded to make sure that prokaryotic initiation is correct?
Definition
GTP hydrolysis.
Term
In prokaryotes, which elongation factor brings in the new aminoacyl-t
Definition
Term
Tu factor elongation is checked by what?
Definition
GTP hydrolysis double-checks codon and anticodon pairing.
Term
After the peptide bond forms, where does the growing peptide move to?
Definition
It is transferred to the tRNA on the A site.
Term
In Translocation, where does everything go? Which elongation factor mediates this? E site tRNA eventually goes where?
Definition
The A site tRNA goes to the P site. The P site tRNA goes to the E site. Elongation factor G mediates this process while hydrolyzing GTP. The deacylated E site tRNA leaves the ribosome.
Term
In prokaryotes, how is termination recognized?
Definition
Release factors recognize stop codons on the mRNA. Triggering termination, they cause the release of the grown peptide to water, rather than the amino acid of another tRNA.
Term
In order to keep translation accurate in prokaryotes, which biochemical opathway is used to insure it?
Definition
GTP hydrolysis
Term
In prokaryotes, where are the three ways in which GTP hydrolysis is used?
Definition
Initiation is at the right place so the right ORF is used.
The correct tRNA matches a codon.
The ribosome advances exactly three codons to prevent a frame shift.
Term
In Eukaryotes, the ribosomes have size of what?
Definition
80s = large subunit is 60s + small subunit 40s.
Term
What is different about the subunits between eukaryotic and prokaryotic translation?
Definition
Eukaryotic subunits are bigger and have larger RNAs. The large subunit has an extra rRNA.
Term
In eukaryotes, where does initiation start?
Definition
The ribosome loading site is the cap on the 5' end. The poly A tail also somehow helps in loading.
Term
What is the initiator sequence?
Definition
It is the the first AUG sequence seen by the ribosome coming in from the 5' cap.
Term
In eukaryotes, how is the intiator tRNA different from prokaryotic initiator tRNA?
Definition
The initiator tRNA is not not formylated. It only contains methionine.
Term
Because eukaryotic and prokaryotic translation is different...
Definition
...drugs can be used as antibacterial agents which target protien synthesis. (Erythromycin & Azithromycin).
Term
After the protein is made, what's next?
Definition
Targeting: we need to figure out where the protien belongs.
Term
Information for protein targeting is where?
Definition
Its read from the amino acids of the protein as it emerges from the ribosome.
Term
Explain the way the protein is secreted?
Definition
The N-terminal sequence initiates the binding of the SRP - signal recognition particle.
Term
After the SRP binds to the ribosome, what happens?
Definition
The ribosome and the growing protein are brought to the ER so that it can be direectly released into the ER.
Term
Protein enter or cross the membrane where?
Definition
At the ER
Term
What does the ER do?
Definition
It does post-translational processing.
Term
Efficient Metabolism and differentiation require what?
Definition
Require control of gene expression.
Term
What are the 2 kinds of transcriptional control?
Definition
Negative control - repressors prevent transcription.
Positive control - activators stimulate transscription
Term
Operon
Definition
Group of genes that are under control of the same regulatory system
Term
Promoter
Definition
transcription start site for RNA polymerase
Term
Operator
Definition
a sequence of DNA to which a regulatory protein binds
Term
Repressor
Definition
a protein that binds to the operator to prevent transcription
Term
Inducer
Definition
a small molecule which makes the repressor leave the operator.
Term
Activator
Definition
A protein that binds to the operator to enhance transcription.
Term
Co activator
Definition
A small molecule that causes an activator to bind to its DNA site
Term
The lac operon is an example of which type of gene control?
Definition
It is prokaryotic gene control.
Term
How many protein does does e.coli have to make in order to metabolize lactose?
Definition
three
Term
Which questions will be asked when the production of lactose metabolism is going to occur?
Definition
Q1: Is there any lactose around for these enzymes to use?
Q2: Is there a better energy source (glucose) available?
Term
For determination of lactose usage - Q1 needs to be answered _____. Q2 needs to be answered _______.
Definition
Q1 needs to be answered yes. Q2 needs to be answered no.
Term
What are the three gene loci for lactose operon?
Definition
lac z, lac y, and lac a
Term
What does lac i code for on the lactose operon?
Definition
Lac i translates the repressor protein.
Term
What is the CAP protein in the lactose operon?
Definition
A global activator whose action is linked to glucose availability.
Term
Which protein is associated with answering of the first question of lactose operon?
Definition
The repressor formed from the lac i.
Term
In the absence of lactose what happens to the attached repressor of the lactose operon?
Definition
The inducer is not attached, and so the the protein is in its repressing conformation: it binds to DNA.
Term
What happens when lactose is availiable in regards to the repressor protein on the operon?
Definition
The inducer is made and attaches to the repressor. This changes the conformation of the repressor and causes the repressor to be released from the operon.
Term
What are the names of the actions done in answering the first question of the lactose operon?
Definition
Repression and Induction
Term
What is question 2 of the lactose operon?
Definition
Is there a better sugar (like glucose) availiable for fuel?
Term
What is the name of the action used to answer question 2 of the lactose operon?
Definition
Positive control
Term
When lactose is absent, the repressor keeps what off the operon?
Definition
It keeps RNA polymerase off the operon the DNA - which stops transcription.
Term
Describe the binding mechanism of repressor. How does it affect timing of attachment and release?
Definition
It has cooperative binding - it attaches on fast and is released fast.
Term
What does CAP stand for?
Definition
Catabolite Activator Protein
Term
What is the master element of the positive control of lactose operon?
Definition
The CAP protein
Term
What does the CAP protein do when there is no glucose in the cell?
Definition
It aids RNA polymerase in recognizing the lac promoter.
Term
How is the activity of CAP regulated through?
Definition
Throught the presence of cAMP.
Term
The default setting of most eukaryotic genes is...
Definition
..off.
Term
What interferes with gene expression when it comes to structure of chromatin?
Definition
The histone-DNA interactions of the nucleosomes can interfere with translation.
Term
In order to loosen the DNA-histone interaction, what needs to be done?
Definition
The histone needs to be acetylated.
Term
What acetylates the histone?
Definition
HAT - histone acetyltransferase.
Term
What are the three things that need to be done to activate the euchromatin? (make it ready for transcription?)
Definition
1.HAT acetylates histones
2.Remodeling engine moves histones.
3.RNA polymerase, transcription factors, activators and mediators attach.
Term
Activator proteins bind to what on the DNA?
Definition
They bind to enhancers: DNA sequences.
Term
Do enhancer-activator complexes act at a distance or locally?
Definition
Act at a distance.
Term
What are all the different locations that an enhancer location can be?
Definition
It can 5' to the intron (upstream) or 3' to the intron (downstream). It can also be found within the neuron.
Term
The enhancer-activator complex binds to what?
Definition
It binds to the mediator and the preinitiation complex.
Term
By the binding of the enhancer-activator complex to the mediator and the preinitiation complex, what happens to the DNA strand?
Definition
It becomes looped over itself.
Term
What DNA-protein complexes limit the action of enhancer-activator complexes?
Definition
Insulators
Term
What is a multicomponent enhancer-activator complex?
Definition
Enhancesome
Term
The Interferon Beta genes has how many kinds of peptides and how many overlapping DNA?
Definition
5 kinds of polypeptides and 8 overlapping sites
Term
Eukaryotic regulatory proteins can be multifunctional. Which means?
Definition
They can act as an activator, repressor of transcription, or repressor of translation.
Term
Whats the significance of needing multiple activators for one promoter?
Definition
It offers combinatorial control; which means that we can use a different combination the enhanceosomes to turn on different genes.
Term
Can a gene have multiple promoters?
Definition
YES.
Term
Activators can be modulated by what else?
Definition
Hormones like estrogen.
Term
On the activator - are there separate sites for DNA and estrogen binding?
Definition
Yes. Estrogen acts as a modulator for activator protein.
Term
When estrogen attaches to the activator protein, what happens to the activator protein?
Definition
It goes through a conformational change which opens the active site for a coactivator to attach.
Term
What are homeotic genes?
Definition
Genes that are controlled by one entire developmental pathway. Mutations of this can cause tissues to become another type of tissue.
Term
What is a segment?
Definition
It is the basic unit of the body plan of insects.
Term
Segment formation in fruit flies is determined by what type of gene group?
Definition
Homeotic genes
Term
Which gene determines the front of each segment?
Definition
The eve gene.
Term
What do reporter genes do in regards to the expression of the eve gene?
Definition
They let you know which of the enhancers have activators attached to them.
Term
What was the reporter gene used for testing activated enhancers of the eve gene?
Definition
Beta - galatosidase gene
Term
At stripe 2, the eve gene has activators. What are they?
Definition
Bicoid and Hunchback
Term
At strip 2, the eve gene has repressors. What are they?
Definition
The repressors are Kuruppel and giant.
Term
How do the repressors repress the eve gene?
Definition
They keep the bicoid and hunchback from binding.
Term
What are the connections of fruit flies to mammalian genes?
Definition
They share homeotic genes.
Term
What are the group of homeotic genes that are similar in arrangement between mice and fruit flies?
Definition
It is the HOX genes. They control the anterioposterior arrangement of the spine.
Term
TOPO cloning is type of way to
Definition
to put DNA fragments into a vector without the use of DNA ligase.
Term
TOPO cling ususally has DNA fragments that were amplified by which two types of polymerases?
Definition
Taq and Pfu.
Term
In TOPO cloning, what is the most important enzyme that breaks the vector and puts allows the PCR products to attach?
Definition
DNA topoisomerase 1.
Term
DNA topoisomerase 1 causes the vector to have what type of ends?
Definition
5'-(c/t)cctt-3'
Term
Monoclonal antibodies are made from which two types of cells fused together?
Definition
differentiated B-lymphocytes and cancer cells. They make a hybridoma.
Term
In random mutagenesis, what happens?
Definition
The DNA is exposed to lots of polymerases and reactive substances to cause mutations.
Term
What do you use for site-directed mutagenesis?
Definition
synthetic oligonucleotides.
Term
What are the 4 ways of getting genes into cells?
Definition
Microinjection of germ cells, electroporation (transformation through an electric shock), transfection (lipid encapsulated DNA), and Viral transduction.
Term
If you designed a peice of DNA, what are two ways that you can insert them into the chromosome?
Definition
Illegitimate (nonhomologous) recombination and General recombination.
Term
What is Illegitimate recombination?
Definition
It is nonhomologous recombination between unrelated types of DNA. It introduce DNA anywhere in the chromosome. It is bad becuase uncontrolled but transposons make efficiency better.
Term
What is general recombination?
Definition
This can deliver DNA to a precise location. The vectors are circular - just needs to match up the sticky ends.
Term
In ecoli, which promoter can we ascribe to certain genes to induce their transcription?
Definition
We can use the lac promoter.
Term
tTA is the what to the Myc oncogene?
Definition
It is the activator.
Term
When mice are treated with tetracycline, what happens to the tTA protein?
Definition
It becomes inactivated - the tetracycline becomes a repressor.
Term
A displaced insulin enhancer/promoter can do what?
Definition
It can turn on neighboring genes, but usually only in pancreatic cells.
Term
What can show succesful incorporation of genes?
Definition
Selectable marker genes and reporter genes.
Term
Site specific recombination can reduce
Definition
problems with verification parts of DNA, since its site specific.
Term
Transgenic Mice has two ways of breeding the gene of interest. What are they?
Definition
Microinjection of germ cells. Embryonic Stem cell Injection.
Term
In the Microinjection of germ cells experiement with transgenic mice, what happens?
Definition
The zygote is injected with the gene of interest. Than the zygote is transplanted into the womb. The progeny trnasgene shown through PCR fragment.
Term
In embryonic stem cell injection, what happens?
Definition
The stem cells of a blastocyst is put into another blastocyst with original stem cells.
Term
The mice progeny that arises from having their stem cells mixed with another mouse's are called what?
Definition
Chimeric mice. They are mosaics of the two original organisms.
Term
What is so good about transgenic mice?
Definition
They allow scientists to knockout sertain genes - act as mouse models of genetic diseases.
Term
What does epigenetics do?
Definition
We can change gene expression by not altering the sequence.
Term
What are three components of epigenetics studied in class?
Definition
1.Gene dosage and X deactivation.
2.Imprinting
3.Environment ability to change epigenetic state.
Term
What are three mechanisms used in epigentics to control gene expression?
Definition
1.Noncoding RNAs (wasted RNAs)
2.DNA methylation
3.Histone modification
Term
Males have one X chromosome, but females have two. How do Drosophila and C.elegans balnce this two?
Definition
Drosophila doubles transcription from the male X. C.elegans halves the transcription rate of each X chromosome.
Term
In activated chromosomes in mammals are called
Definition
Barr bodies
Term
The Barr resembles what?
Definition
Heterochromatin
Term
When is the inactivated X chromosome chosen during development?
Definition
It is chosen early in embryogenesis.
Term
How is the agouti gene controlled in mice?
Definition
If methylated it represses expression, it can cause variegated expression of mottled gene.
Term
Heterochromatin is transscriptionally active or inactive.
Definition
Transcriptionally inactive.
Term
X inactivation in mammals is similar to what we see in
Definition
drosophilia
Term
In activations starts where on the chromosomes?
Definition
It starts at the center and drops off with distance.
Term
What does Xist mean?
Definition
X-inactive specific transcript.
Term
What does Xist do?
Definition
It coats the Barr body, establishing inactivation. Some genes are still on though (Xist gene).
Term
If xist RNA is removed, is the Barr body still inactivated?
Definition
Yes.
Term
What is the complement and opposer of Xist?
Definition
Tsix
Term
What is imprinting?
Definition
Imprinting is when certain genes behave differently because they were inherited from the mom or dad.
Term
What does igf2 stand for?
Definition
Insulin-like growth factor.
Term
The paternal gene for Igf2 is
Definition
downregulated. It is only expressed by the father's genes.
Term
The maternal gene for Igf2 receptor is
Definition
downregulated. It is only expressed by the mother's gene.
Term
If the igf2 gene is lost then what happens?
Definition
The baby and the placenta will be very small.
Term
If the loss of the Igf2 receptor leads to what?
Definition
Large offspring.
Term
In the imprinting experiment, the transgene was inserted where?
Definition
Into the immunoglobulin locus.
Term
How did insertion of the c-myc gene show imprinting?
Definition
Only males expressed the gene, females repressed it through imprinting.
Term
How was the c-myc gene repressed through imprinting by the females?
Definition
The gene was methylated.
Term
Methylation prevents what enzyme from doing what?
Definition
It prevents restriction enzymes from cutting their sites.
Term
Maternally inherited transgenes are always...
Definition
methylated, regardless of the methylation state of the mother.
Term
Paternal transgenes are always
Definition
unmethylated. Regardless of the methylation state of the father.
Term
Artificail methylation can...
Definition
turn off gene expression when needed.
Term
With what does histone deacylate?
Definition
With a methyl-binding domain it deacetylates a methylcytosine-containing chromatin.
Term
Methyl transferases recognize what?
Definition
CpG.
Term
What does methyl transferases do to CpG?
Definition
It fully methylates them.
Term
What the problem with methyl-cytosine?
Definition
It can deaminate to thymine. Mutations can result.
Term
Methylation can turn off...
Definition
insulators - causes expression.
Term
Children of mother's who survived the hunger winter had what?
Definition
Had different DNA methyaltion patterns whicj were different than their siblings.
Term
Changes in the imprinting patterns in twins are associated with...
Definition
observable differences between twins.
Term
Rhodopsin is what kind of receptor?
Definition
7TM receptor. G Protein Coupled receptor.
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