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Chapter 2
Genes and Chromosomes
Questions:
1.
What is different between gene cluster or gene family?
2.
Can you explain why A does not base-pair with C, and why T does not base-pair with G?
3.
The chemical structure of U is simpler than T. So, we understand why RNA uses U,
instead of T. A can pair with U as perfectly as with T. However, why does DNA use T?
Why dose DNA choose a more complex base?
4.
Why do we choose those organisms as model organisms?
5.
Is the junk DNA real junk?
6.
What is Klenow fragment?
7.
Is DNA replication conservative or semiconservative?
8.
In semiconservative replication, what fraction of the DNA consists of one original parent
strand and one daughter strand after 1, 2, and 3 rounds of repocation?
9.
In which mode of replication does a parent circular DNA molecule yield two daughter
circles?
10.
In which mode of replication does a parent circle generate a circle with a linear branch?
11.
Name three enzymatic activities of DNA polymerase I.
Multiple Choice:
(1)
A
B
C
D
The number of replicons in a typical mammalian cell is?
40-200
400
1000-2000
50000-100000
(2)
A
B
C
D
In prokaryotes, the lagging strand primers are removed by?
3’-5’exonuclease
DNA ligase
DNA polymeraseⅠ
DNA polymerase Ⅲ
(3)
A
B
C
D
The essential initiator protein at the E.coli origun of replication is?
DnaA
DnaB
DnaC
DnaE
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(4)
A
B
C
D
Which phase would a cell enter if it was starved of mitogens before the R Point?
S
G1
G2
G0
(5)
A
B
C
D
What is important for a prokaryotic plasmid to replicate in yeast cell?
ORC
CDK
ARS
RNA
(6) In methyl-directed mismatch repair in E.coli, the daughter strand containing the
mismatched base is nicked by?
A MutH endonuclease
B UvrABC endonuclease
C AP endonuclease
D 3’-5’exonuclease
(7) Which of the following correctly describes A-DNA ?
A A right-handed antiparallel double helix with 10bp/turn and bases lying perpendicular
to the helix axis.
B A left-handed antiparallel double helix with 12bp/turn formed from alternating
Pyrimidine purine sequences.
C A right-handed antiparallel double helix with 11bp/turn and bases tilted with Respect
to the helix axis.
D A globular structure formed by short intramolecular helices formed in a single
stranded nucleic acid.
(8)
A
B
C
D
E
F
Which are the major classes of DNA repair processes?
nucleotide excision repair
base excision repair
mismatch repair
recombinational repair
error-prone repair
reversal of damage
(9)
A
B
C
D
Denaturation of double strand DNA involves?
Breakage into short double-stranded fragments
Separation into single strands
Hydrolysis of the DNA backbone
Cleavage of the bases from the sugar-phosphate backbone
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(10)
A
B
C
D
The characteristic of typeⅠDNA topoisomerases:
chang linking number by ±2.
require ATP.
break one strand of a DNA double helix.
are the target of antibacterial drugs.
(11)
A
B
C
D
Which of the following is common to both E.coli and eukaryotic chromosomes?
The DNA is circular.
The DNA is packaged into nucleosomes.
The DNA is contained in the nucleus.
The DNA is negatively supercolied.
(12)
A complex of 146bp of DNA with the histone octamer plus histone H1 is known
as :
nucleosome core
solenoid
30nm fiber
chromatosome
A
B
C
D
(13)
A
B
C
D
Which of the following is an example of highly-repetitive DNA?
Alu element
histone gene cluster
DNA minisatellites
dispersed repetitive DNA
(14)
A
B
C
D
Which has the highest absorption per unit mass at a wavelength of 260nm?
double–stranded DNA
mononucleotides
RNA
protein
(15)
A
B
C
How to distinguishing single-stranded (ss) from double-stranded (ds) DNA?
Spectrophotometrically
Some nucleases are essentially specific for single-stranded nucleic acids
HAP (hydroxyapatite) column
(16)
A
B
C
D
Which of the following is not a nucleoprotein?
keratin
chromatin
histone
proteoglycan
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Chapter 3
Transcription (DNA → RNA)
Questions
1. How many steps are required for the expression of RNA genes?
2.
How many steps are required for the expression of protein genes?
3.
Which DNA strand is able to be read by RNA polymerase in transcription?
4.
Is the “Stop” codon in the genetic code a signal for the end of transcription?
5. How to determine the sequence of promoter?
6.
Describe the differences between DNA polymerase and RNA polymerase.
7.
a. What is mRNA?
b. How does mRNA sometimes differ from a primary transcript?
c. Define cistron and polycistronic mRNA.
d. Which parts of a mRNA molecule are not translated?
8.
9.
Answer these questions about eukaryotic RNA.
i.
What is a cap?
ii.
At which end of the mRNA is the poly(A)?
iii.
Are there eukaryotic mRNA molecules that do not contain either feature?
What is mRNA ‘splicing’ and RNA ‘editing’?
10. How many types of RNA splicing? What are their procedures?
11. Define cistron and polycistronic mRNA
Multiple Choice:
(1) The sequence 5’-AGTCTGACT-3’in DNA is equivalent to which sequence in RNA?
A 5’-AGUCUGACU-3’
B 5’-UGTCTGUTC-3’
C 5’-UCAGUCUGA-3’
D 5’-AGUCAGACU-3’
(2)
A
B
C
D
In what region of the interphase chromosome does transcription take place?
the telomere
the centromere
euchromain
heterochromain
(3) Which are right about mRNA structure in eukaryotes?
A They are capped at their 5' ends and polyadenylated at their 3' ends.
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B All thef mRNAs have poly A at the 3' end.
C The poly A tail at the 3' end can be used to purify mRNAs from other RNAs.
(4) Which two of the following statements about transcription are correct ?
A RNA synthesis occurs in the 3′ to 5′ direction.
B the RNA polymerase enzyme moves along the sense strand of the DNA in a 5′ to 3′
direction.
C the RNA polymerase enzyme moves along the template strand of the DNA in a 5′ to 3′
direction.
D the transcribed RNA is complementary to the template strand.
E the RNA polymerase adds ribonucleotides to the 5′ end of the growing RNA chain.
F the RNA polymerase adds deoxyribonucleotides to the 3′ end of the growing RNA
chain.
(5)
A
B
C
D
Which one of the following statements about E.coli RNA polymerase is false?
the holoenzyme includes the sigma factor.
the core enzyme includes the sigma factor.
it requires Mg2+ for its activity.
it requires Zn2+ for its activity.
(6)
A
B
C
D
E
F
Which one of the following statements is incorrect?
there are two α subunits in the E.coli RNA polymerase.
there is one β subunits in the E.coli RNA polymerase.
E.coli has one sigma factor.
the β subunits of the E. coli RNA polymerase is inhibited by rifampicin.
the streptolydigins inhibit transcription elongation.
heparin is a polyanion, which binds to the β subunit.
(7) Which one of the following statements is true?
A RNA Pol Ⅱ only transcribes protein-coding genes.
B The TATA box has a role in transcription efficiency but not in positioning the start of
transcription .
C TBP binds to the TATA box.
D Enhancers typically lie 100-200 bp upstream from the start of transcription.
(8)
A
B
C
D
E
Which one of the following statements about general transcription factors is false?
TFⅡD binds to the TATA box.
TFⅡD is a multiprotein complex consisting of TBP and TAFs.
TBP is a common factor in transcription by RNA Pol ,RNA Pol Ⅱ,RNA Pol Ⅲ.
TFⅡB stabilizes the TFⅡD-DNA complex.
TFⅡE,TFⅡH,TFⅡJ associate with the transcription complex after RNA polymerase
binding.
F TFⅡH phosphorylates the CTD.
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Chapter 4
Translation (RNA → Protein)
Questions
1. Which of the following properties are part of the normal functioning of aminoacyl tRNA
synthetases?
(a) Recognition of the codon
(b) Recognition of the anticodon of a tRNA molecule
(c) Recognition of the amino acid recognition region of a tRNA molecule
(d) Ability to remove an incorrectly coupled amino acid from a tRNA molecule
2. What are the values of prokaryotic and eukaryotic ribosomes, their subunits, and their
tRNA molecules?
3. Which of the following are steps in protein synthesis in prokaryotes? If false, explain.
(a) Binding of tRNA to a30S particle
(b) Binding of tRNA to a70S ribosome
(c) Coupling of an amino acid to ribosome by an aminoacyl synthetase
(d) Separation of the 70S ribosome to form 30S and 50S particles
4. Translation has evolved in a particular polarity with respect to the mRNA molecule. What
is this polarity, and what would be the disadvantages of having the reverse polarity?
5. Which of the following is the normal cause of chain termination?
(a) The tRNA corresponding to a chain-termination triplet cannot bind an amino acid.
(b) There is no tRNA with an anticodon corresponding to a chain-termination triplet.
(c) Messenger RNA synthesis stops at a chain termination triplet.
6. How dose molecular chaperone work?
7.
How dose ubiquitin degrade protein?
8. How dose proteasome work?
Multiple Choice:
(1) Which are the secondary structure of tRNA?
A It is not a cloverleaf.
B tRNAs have 4 arms with 3 loops.
C The amino acid acceptor arm is formed by complementary base-pairing
between the intial 7 nts of tRNA and a short segment near the 3' end.
D The anticodon arm ends in anticodon loop.
E The variable loop varies in size in different tRNAs.
F The TC arm is named for this highly conserved motif found in the loop.
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(2) Which are the roles of ribosomes?
A Ribosomes are the molecular machines that catalyze peptide bond formation between a
growing polypeptide and an incoming aminoacyl-tRNA.
B The ribosomes insures that the amino acids are added in the order specified
by the mRNA.
C Ribosomes associate reversibly with the tRNA.
(3) The tRNA interacts with the ribosome at three major sites, which is right?
A P site (or entry site): aminoacyl- tRNA binds
B A site (or donor site): peptidyl-tRNA binds, i.e. the nascent polypeptide
chain linked to the last tRNA to occupy the A site
C E site: exit of deacylated tRNA after peptide bond formation
(4) The statements about Initiation Factor 3(IF-3) are as follows, which is right?
A An antiassociation factor; prevents association between the large and
small ribosomal subunits.
B It also must be associated with the small subunit for it to form an
initiation complex, i.e. for the small subunit to correctly bind mRNA
and fmet-tRNAf.
C Brings fmet-tRNAf to the partial P site on the small subunit.
D It dissociates prior to binding of the large subunit.
(5)
A
B
C
What is the action of tetracycline in prokaryotes?
It blocks translocation reaction on ribosomes.
It blocks peptidyl transferase reaction on ribosomes.
It blocks the binding of amino-acyl tRNA to the A site of ribosomes.
(6)
A
B
C
D
E
F
E.coli release factor1(RF1) recognizes which codons?
UAA only
UAG only
UGA only
UGA and UAA
UAG and UAA
UAG and UGA
(7) Which one of the following protein synthesis factors are not equivalent pairs in
prokaryotes and eukaryotes ?
A EF-G; Eef2
B EFC RF1 and RF3; eRF
D EF(8) Which one of the following statements about post-translations events is false?
A some mRNA encode polyproteins.
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B protein targeting involves signal sequences in the nascent polypetides.
C signal peptidase removes one or two amino acids from the amino terminus of some
proteins.
D proteins can be modified by acetylation, phosphorylation and glycosylation.
(9) Which of the following is the normal cause of chain termination?
A the tRNA corresponding to a chain-termination triplet cannot bind an amino acid.
B there is no tRNA with an anticodon corresponding to a chain-termination triplet.
C messenger RNA synthesis stops at a chain termination triplet.
(10) Which of the following properties are part of the normal functioning of aminoacyl
tRNA synthetases?
A recognition of the codon
B recognition of the anticodon of a t RNA molecule
C recognition of the amino acid recognition region of a tRNA molecule
D ability to distinguish one amino acid from another
E ability to remove an incorrectly coupled amino acid from a Trna molecule
Chapter 5
Structure & Function of Protein
Questions
1.
What are the differences between protein tertiary structure and quaternary structure?
2.
What are the differences between motif and domains of protein structure?
3. What are the differences between gene family and protein family?
4.
How dose an unfolding polypeptide fold into a native protein folding?
5.
What are causes of protein misfolding?
6.
What is the relationship of enzyme structure and function?
Multiple Choice:
(1) The specific activity of an enzyme would be reported in which of the following units
of measure?
A Millimoles per liter
B Units of activity per milligram of protein
C Micromoles per minute
D Units of activity per minute
E Milligrams per micromole
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(2) The functions of many enzymes, membrane transporters, and other proteins can be
quickly activated or deactivated by phosphorylation of specific amino acid residues
catalyzed by enzymes called
A Cyclases
B Kinases
C Phosphatases
D Proteases
E Zymogens
(3)
A noncompetitive inhibitor of an enzyme
A Increases Km with no or little change in Vmax
B Decreases Km and decreases Vmax
C Decreases Vmax
D Increases Vmax
E Increases Km and increases Vmax
(4) Which of the following statements about solutions of amino acids at physiologic pH
is true?
A All amino acids contain both positive and negative charges
B All amino acids contain positively charged side chains
C Some amino acids contain only positive charges
D All amino acids contain negatively charged side chains
E Some amino acids contain only negative charges
(5) The highest concentration of cystine can be found in
A Melanin
B Chondroitin sulfate
C Myosin
D Keratin
E Collagen
(6) Which of the following amino acids is ionizable in proteins?
A Leucine
B Histidine
C Valine
D Alanine
E Glycine
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Practice of viewing the stereo illustration of 3D-protein
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Chapter 6 & 7
Regulation of Genes Expression
in Prokaryotes and Eukaryotes
Questions：
1. How is gene expression regulated?
2. How do induction and repression work to regulate microbial metabolism
3. Describe positive and negative control in transcription level of regulation
4. How does lac operon work to regulate lactose metabolism
5. Give an example of attenuation
6. Describe the difference of gene expression between prokaryotes and eukaryotes
7. What are the main features of repressor and corepressor?
8. Explain how the regulatory protein AraC can be both a repressor and an activator.
9. Why does attenuation not occur in eukaryotes？
10. List two mechanisms a bacterial cell uses to control the amount of mRNA present inside
the cell.
11. What RNA polymerase(s) transcribe eukaryotic genes? Name the polymerase(s) and the
type of gene(s) it transcribes.
12. In prokaryotes, regulatory elements are fixed positions with respect to the gene(s)
regulated. How does the situation differ in eukaryotes ?
13. List several mechanisms a cell uses to increase the concentration of a particular mRNA
molecule to a very high value.
14. How might a cell be signaled to synthesize one particular protein, but no other?
15. If an enhancer were moved from a position near gene A, where it has strong enhancing
activity, to a position 50 nucleotides upstream from gene B, which is constitutively
transcribed, would transcription of gene B be increased?
16. In prokaryotes, positive regulatory elements often provide a binding site for RNA
polymerase, which strengthens the binding of the polymerase to the transcription start site.
What is the evidence that suggests that most eukaryotic regulatory elements function
differently?
17. What is antisense RNA and its applications?
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Multiple Choice：
(3)
A
B
C
D
Which element of the followings effects in the regulation of Trp operon?
Enhancer
Transcriptor
Cistrsn
Attenuator
(4)
A
B
C
D
In the lactose operon , which of the followings the repressor combine with?
Promotor gene
Operator gene
Strctural gene
Others
(5)
A
B
C
D
DNA methylation would:
Close some genes
Activate some genes
Close some genes and activate some genes
Have nothing to do with gene regulation
(6)
A
B
C
D
E
The DNA binding domains of trans-acting factor includes:
Helix-turn-helix
Zinc finger
Basic-leucine zipper
Basic-heix/loop/helix
Homeo domains
(7) Which statement of the followings about chaperonine is right?
A It is one kind of inorganic molecule
B It is one kind of necletic acid
C It is one kind of protein
(8)
The presence of which of the following structural arrangements in a protein
strongly suggests that it is a DNA-binding regulatory protein?
A β-sheet
B Triple helix
C α-helix
D Zinc finger
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Chapter 8 New Research Field in Molecular Biology
Questions
1.
How to classify proteins into functional classes?
2.
How to compare one proteome with another?
3.
How to include functional/activity/pathway information in databases?
4.
How to extract functional motifs from sequence data?
5.
How to predict phenotype from proteotype? Genotype (基因型)→ Proteotype(蛋白型)
6.
How to correlate changes in protein expression with disease?
7.
How to distinguish important from unimportant changes in expression?
8.
How to compare, archive, retrieve gel data?
9.
How to rapidly, accurately identify proteins from MS and 2D gel data?
10.
How to include expression info in databases?
11.
How to predict 3D structure from 1D sequence?
12.
How to determine function from structure?
13.
How to classify proteins on basis of structure?
14.
How to recognize 3D motifs and patterns?
15.
How to use bioinformatics databases to help in 3D structure determination?
16.
How to predict which proteins will express well or produce stable, folded molecules?
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