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Biochemistry 2280A Lecture Notes - Lecture 17: Trp Operon, Sigma Factor, Consensus Sequence

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School
Western University
Department
Biochemistry
Course
Biochemistry 2280A
Professor
Boffa/ Mc Lauchlin/ Brandl

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Document Summary

Topic 17 & 18: prokaryotic and eukaryotic transcription & gene regulation. Information is stored in dna in the form of genes. Identify the structural characteristics of some bacterial dna-binding proteins. Describe the components needed for transcription in bacterial cells. Describe mechanisms for transcriptional activation and repression in bacteria. The human genome encodes ~21,000 different protein encoding genes. The expression of the correct genes is essential for growth and differentiation. Most disease states, most notably cancer, are due to altered expression of one or more genes: wrong amount or wrong location. By therapeutically manipulating gene expression, we have the potential to prevent or reverse disease. The central dogma dna rna protein. If no rna intermediate, each gene would be equally present 2 copies per gene for diploids: rna can vary from less than one to over 1000 copies per cell. Since rna can be degraded, expression of a gene can be stopped quickly: good on/off switch.

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Related Questions

22. What is probably the single most important distinction between bacteria and eukaryotes?

a. transcription

b. the separation of the cell's genetic material from the surrounding cytoplasm

c. the existence of ribosomes

d. RNA processing in bacteria

e. antibiotics

23. Which one does NOT characterize an open reading frame (ORF)

a. Uses six reading frames during translation

b. Contains a start codon

c. Contains a stop codon

d. Its length is in multiples of 3 nucleotides

e. It should have the number of codons for a protein or on average ~250 codons in length.

24. Nested intronic genes lie within the non-coding intronic region of a larger gene, and occur in the human genome.

a. True

b. False

25. How would you characterize this statement: EF-Tu will hydrolyze GTP only if the codon:anticodon & tRNA:amino acid matchings are correct

a. Transcription; initiation steps

b. Transcription; termination steps

c. Translation: initiation steps

d. Tanslation: elongation steps

e. Spliceosome

26. Regarding the transcription unit architecture of the Escherichia coli genome, which one is FALSE?

a. Each of the 4,661 transcription units comprised an average of 1.1 modular units.

b. 3,010 transcription units (~65%) are monocistronic.

c. 1,652 transcription units (35%) contain more than one ORF (polycistronic)

d. The largest transcription unit is equivalent to 16 ORFs with numerous introns.

e. 398 transcription units (~9%) are nested within each other in opposite transcriptional orientation

27. Regarding RNA interference (RNAi), which one is FALSE?

a. It is a common and conserved mechanism in eukaryotic cells.

b. Originally discovered in bacteria and plant viruses.

c. A form of primitive immunity to protect the genome.

d. Pre microRNA (miRNA) genes have been found in introns.

e. Recent research shows that exogenous plant miRNAs in food can regulate the expression of target genes in mammals.

28. Aminoacyl-tRNA synthetases

a. Recognize the 3’UTR

b. The genes for these enzymes fall into the family of inducible genes

c. The enzymes are imported into the nucleus

d. Covalently attaches an amino acid to the appropriate tRNA. This takes place in the cytoplasm.

e. Forms the peptide bond during protein synthesis

29. What is the process by which complementary RNAs are made from a DNA template?

a. translation

b. transcription

c. protein synthesis

d. transduction

e. transliteration

13

Which of the two major categories of the chemical reactions in photosynthesis is oxygen the INDIRECT product?

A

Glycolysis

B

Oxidative phosphorylation

C

Both light and dark

D

Light independent phase (LIP)

E

Light dependent phase (LDP)

14

You have a stomach flu characterized by vomiting. Which of the following systems is most responsible for the food in your stomach going the wrong way, e.g. vomiting? (Disregard this question and answer choice B)

A

Cardiac Muscle in the large intestine as discussed in class.

B

Smooth muscle in the gastrointestinal tract

C

Smooth muscle in the blood vessels

D

Skeletal muscle in the intestine

15

Proteins are made from which of the following smaller sub units?

A

Nucleotides

B

Amino acids that cannot enter the blood stream and go to cells

C

Monosaccharides

D

Fatty acids

E

Amino acids which can form new protein

16

Carbohydrates are digested in the gastrointestinal system into which of the following substances that is the smallest structure?

A

Polysaccharides that are produced by glucagon

B

Monosaccharides that are produced by insulin

C

Monosaccharides

D

Polysaccharide

17

Which of the following biomolecules has the longest digestion time? In other words, how long does it take for the biomolecule to be catabolized?

A

DNA

B

Lipid

C

Carbohydrate

D

Protein

18

You are sunburned after a long day at the beach. Which one is not an example of UV damage to your skin cells?

A

A mutation can occur in your ovaries

B

A mutation can occur in skin cell DNA that can lead to errors in transcription.

C

Errors can occur during DNA replication.

D

UV light can cause mutations in DNA of skins cells.

E

Thymine bases in your skin DNA bond with each other instead of across the double helix

19

This region, the ______________ (a) tells RNA polymerase where to bind to DNA while this region, the ______________ (b) tells RNA where to start transcription.

A

(a) promoter, (b) open reading frame

B

(a) start codon, (b) methionine

C

(a) promoter, (b) start site

D

(a) start site, (b) promoter

20

The genetic code is used to translate ______________ into ______________.

A

lipids, nucleotides

B

nucleotides,carbohydrates

C

nucleotides, lipids

D

nucleotides, amino acids

E

nucleosides, amino acids

21

Transcription of a gene has just completed. What are the next steps (in the correct order) to complete expression of that gene?

A

RNA polymerase makes a copy of DNA into mRNA.

B

mRNA is translated in the nucleus and ribosomal RNA moves into the cytoplasm.

C

Gene expression is completed after transcription.

D

mRNA moves into the cytoplasm and with tRNA they interact to form protein

E

Translation machinery moves into the nucleus and mRNA is translated into protein.

22

How is it that a mutation in DNA stored inside the nucleus of a cell can cause a disease affecting multiple organs?

A

This remains an unanswered question in science that scientists are still trying to figure out.

B

The mutated DNA is expressed in multiple cells through the process of transcription and translation, and the altered protein causes the disease wherever the DNA was expressed.

C

The mutated DNA is expressed in one cell and the altered protein travels to multiple organs to cause disease.

D

The mutated DNA is expressed and the mRNA takes the mutated information to other cells where the altered protein is made to cause disease in that organ.

23

The advantage of sickle cell anemia is which of the following?

A

It decreases the amount of oxygen in the blood cells so that mosquitoes carrying malaria will live

B

It decreases the amount of oxygen in the blood cells so that mosquitoe's blood form will die.

C

It allows the blood vessels to decrease the amount of blood going to the toes and feet.

D

There is none.

24

Which of the following is a purpose of cell division?

A

Cell reproduction

B

Growth

C

Repair

D

All of these

Expression vectors inprokaryotes do not make functional eukaryotic gene products inbacteria very well because

Answer Not sure which one ?!

· the codon sequence for prokaryotes is differentthan the codon sequence in eukaryotes

· there are no disulfide bridges formed in proteinsnormally made in prokaryotes

· prokaryotic expression vectors cannot translateeukarytic sequences

· eukaryotic genes have introns, and prokaryotesdon't

· eukaryotic genes have exons and prokaryotesdon't


I create a knockout mouseusing the agouti/black fur system \. When I cross the agoutioffspring of the originally engineered mouse, I find a ratio of 2agouti mice to 1 black furred mouse. What is the bestexplanation?

Answer not sure which one?!

· The gene knocked out was recessive.

· The gene knocked out was dominant.

· The gene knocked out was a lethalgene.

· The knockput was integrated into a random spot,and did not knockput the original gene.

A restriction enzyme cuts DNAand leaves the following end

xxCTGCA
xxG

Which of the following could be the sequence of the correspondingend of the other end of the cut DNA?

Answer

· xxG
xxCTGCA

· xxC
xxGTGCA

· xxCCGAT
xxG

· xxGGCTA
xxC


An SNP always occurs dueto

Answer

· a one base-pair change.

· a three base-pair change.

· a single restriction site change.

· a single amino acid change.

· None of these.


I PCR out a mutated gene in apatient with Lisenbee chorea (the inability to dance in acoordinated fashion) and I compare it to another patient with thatsame disease phenotype. One subject had a mutation on chromosome 4,and the other subject couldn't rock it because of a mutation onchromosome 5. This is an exampe of

Answer

· pleitropy

· locus heterogeneity

· allelic heterogeneity

· dominant negative mutation

· penetrance

In his experiments, Mendelnoted that when two traits are involved in a genetic cross, theyare inherited independently of each other. Though Mendel didn'tknow about chromosomes, this still holds true (mostly)because

Answer

· genes on the same chromosome are often mixedthrough meiotic crossover during the formation ofgametes.

· variant alleles of the same gene do not interferewith the phenotypic expression of the gentoype in different geneticloci.

· most higher organisms are diploid, making only twoalleles available for every genetic locus, and there is a 50/50chance of geting either allele from a single parent.

· expression of phenotypes can vary from thegenotypes because of encironmantal influences.

· chromosomes often recombine

Anticipation is caused by amutation that increases in expressivity over subsequentgenerations.

Answer

· True

· False

Question 44

I have a genotype that shouldproduce a specific phenotype, but some of the individuals with thegenotype do not demonstrate any evidence of the phenotype. I wouldconsider this an example of

Answer

· allelic heterogeneity.

· locus heterogeneity.

· penetrance.

· expressitivity.

· sheer luck.

Question

Which of the following doesnot occur during the PCR reactions?

Answer

· Changes in the reaction temperature by athermocycler

· Denaturation at high temperatures

· Synthesis of oligonucleotide primers

· Extension of primers by DNA polymerase

· Annealing of oligonucleotide primers

Question

DNA markers, or variantnon-coding regions of DNA, are DNA polymorphisms that are usefulfor genetic mapping.

Answer

· True

· False

A mosaic is an organismwith

Answer

· multiple genotypes within one organism

· multiple alleles within one genotype

· more than one color of fur

· transgenes added to the zygote beforedevelopement

· a wt phenotype but a mutated genotype

Question

Genotype causesphenotype.

Answer

· No, gentoype just influences phenotype.

· Yes, genotype is the DNA sequence that createsphenotype.

Question

A true genetic chimera can becreated by

Answer

· mutating a gene early on in the development of anorganism resulting in different alleles being present in theadult

· multiple fertilized eggs or zygotes fusing to formone embryo

· adding a transgene to the genome of an organismduring fetal development only

· adding cells of a different species to an adultorganism

· adding a transgene to the genome of an animal atany stage in development

Question

The ABO blood group can bestbe explained by the concept of _______.

Answer

· dominant traits

· recessive traits

· allelic heterogeneity

· locus heterogeneity

· vampirism

If a loss of functionmutation creates a dominant phenotype, it may be becauseof

Answer

· haploinsufficiency

· penetrance

· expressivity

· allelic heterogeneity

· locus heterogeneity

Please select the best matchfor each.

Answer

· PCR: Technique used to generatecopies of a DNA fragment

· Southern blot : Screeningprocedure used to assay DNA fragments

· RFLPs : DNA fragments generatedby restriction enzymes that vary in length betweenindividuals

· Northern blot : Screeningprocedure used to assay mRNA fragments

· Electrophoresis Movement ofmacromolecules in an electrical field

Answer

A.

Screening procedure used toassay DNA fragments

B.

Movement ofmacromolecules in an electrical field

C.

Screening procedure used toassay mRNA fragments

D.

DNA fragments generated byrestriction enzymes that vary in length betweenindividuals

E.

Technique used to generatecopies of a DNA fragment

A gene mutates, and theprotein produced has a novel way of interacting with the cell, andcreates a new phenotype because of this new functionality. This iscalled

Answer

· pleitropy

· locus heterogeneity

· allelic heterogeneity

· dominant negative mutation

· gain of function dominant mutation

Question 62

Mutations in the somaticchromosomes may be inherited by the next generation.

Answer

· True

· False


A degenerate PCR primer withmany variant sequences must be used to make multiple copies of agene

Answer

· if only the protein sequence of the gene productis known to construct the primers

· if the DNA you are using is cDNA to constructthe primers

· if the DNA you are using is genomic DNA to becopied

· if the DNA you are trying to copy iscDNA

· if the vector is prokaryotic and the transformedcell is eukarytotic

Question

Please select the best matchfor each term.

Answer

· Restriction enzyme


· PCR C

· Plasmid

· YAC A

· Dideoxynucleotide

Answer

A.

Endonuclease isolated frombacteria

B.

Eukaryotic cloningvector

C.

Method for amplification ofDNA sequences

D.

Small circular fragment ofDNA

E.

Molecule used in DNAsequencing

Question

A couple goes on MauryPovitch, and the results are in: you are not the father. But noother man impregnated the female (granted, unlikely for a MauryPovitch guest, but work with me here) and he must be the father.DNA analysis claims otherwise, though the child definitely wasmom's (poor thing). What may be going on here?

Answer

· the child is parthenogenic because the motheractually impregnated herself like a shark, and the child's DNA isall mom's

· the child had a mutation that changed the genethat is used to trace paternity

· the child is a mosaic because he is actually a setof twins fused early during fetal development, and therefore camefrom 2 eggs and 2 sperm

· the dad may have germ-line mosaicism, meaning thatthe genotype of his sperm is different from his somaticgenotype

· mitochondrial DNA only comes from mom, so there isno way to tell whobthe baby's father is