Study questions I

Chapter 11-12-12

1. DNA polymerase III adds nucleotides ________.

A) to the 3′ end of the RNA primer
B) to the 5′ end of the RNA primer
C) in the place of the primer RNA after it is removed
D) to both ends of the RNA primer
E) to internal sites in the DNA template

2. DNA polymerase I is thought to add nucleotides ________.

A) to the 5′ end of the primer
B) to the 3′ end of the primer
C) in the place of the primer RNA after it is removed
D) on single-stranded templates without need for an RNA primer
E) in a 5′ to 5′ direction

3.
(a)

(b)

4. Given that the nature of DNA replication in eukaryotes is not as well understood as in
prokaryotes,
(a) present a description of DNA (chromosome) replication as presently viewed in eukaryotes
and
(b) state the differences known to exist between prokaryotic and eukaryotic DNA replication.
 5. What is the name of the replication unit in prokaryotes, and how does it differ in
eukaryotes?

6. Which of the following promotes strand exchange?

a) DBS formation
b) Heteroduplex formation
c) Strand invasion protein
d) Branch migration

7. What is gene conversion?

8. What term is used to describe genetic exchange at equivalent positions along two
chromosomes with substantial DNA sequence homology?

9. Describe the function of the RecA protein.

True or False:
10. G-quartets are G-rich single-stranded tails that loop back on themselves forming G-G
double stranded sections. Such looping is involved in aligning chromosomes for
homologous recombination.

11. A nucleosome is a structure associated with the nuclear membrane. It helps maintain a
stable relationship between the extracellular matrix and the membrane itself.

12. Viral genomes are always linear, double-stranded DNA.

13. Telomerase is an enzyme involved in the replication of the ends of eukaryotic

chromosomes.

14. In situ hybridization allows one to "visualize" the location of labeled RNA or DNA in a
tissue or cell.

15. In contrast with euchromatin, heterochromatin contains more genes and is earlier
replicating.
 16. Each human contains an identical set of VNTRs.

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17. Chromosomal regions that represent evolutionary vestiges of duplicated copies of genes
that have underdone sufficient mutations to render them non-functional are called
________.

18. What are SINE and LINE elements? Why are they called "repetitive"?

19. What are minisatellites and microsatellites? Do they have any use?

20. Describe the basic structure of a nucleosome. What is the role of histone H1?

21. Compare and contrast the chromosome structure of viruses, bacteria, and eukaryotes.

22. How does a polytene chromosome differ from a typical eukaryotic chromosome?

23. In human chromosomes, satellite DNA sequences of about 170 base pairs in length are
present in tandem arrays of up to 1 million base pairs. Found mainly in centromere
regions, these DNA sequences are called ________.

24. How is the solenoid structure formed?

25. Describe how chromatin remodeling can take place.

26. The genetic code is said to be triplet, meaning that there ________.
A) are three amino acids per base in mRNA
B) are three bases in mRNA that code for an amino acid
C) may be three ways in which an amino acid may terminate a chain
D) are three "nonsense" triplets
E) none of the above
 27. Below is the mRNA sequence for a gene called FBG (FRODOBAGGINS). find the
information about the mRNA

1 ugcuuagcac cuaucugcuc ucuggccugc cucagugguc uacagcaguu acacacaggc

61 agugguaucu gugagcagcu cuguggacuc aaagguuuuc ucccugagag gcaugaccca
121 ggccagcuga uucaucagaa ucaggaugga cgugguagag gucgcgggua guuggugggc
181 acaagagcga gaggacauca uuaugaaaua cgaaaaggga caccgagcug ggcugccaga
241 ggacaagggg ccuaagccuu uucgaagcua caacaacaac gucgaucauu uggggauugu

1861 cauccucguu uuauuuuugg uuaaacuuau gaaaauguau uaagaaagag ugcagcucga

1921 gagagauuca gagauggaac acaccagacc ccagaucaca aagccaacca ugcccagccc
1981 cucccagcac ccccagcccc acgaccaucg uucugaauuc ugacgacacc gugagccugc
2041 cuuuguacuu caaacucaug gaaggauaac caccuucaug uuuugaaaua aauguuuccu
2101 guugaaauga aaaaaaaaaa aaaaaaaaaa aaaaa

Coordinates
mRNA 1..2135
Coding sequence 146..1795

a. How many amino acids are there in this protein? ………………

b. What are the size of 5’ and 3’ UTRs? ………………

 28. You are given the following piece of DNA molecule. First strand is the template strand
for RNA polymerase.

Strand 1: 5’ATGCGCTACGGCAAT 3’
Strand 2: 3’TACGCGATGCCGTTA 5’

UUU Phe UCU ser UAU tyr UGU cys

UUC UCC
UUA leu UCA UAC stop UGC stop
UUG UCG UAA stop UGA trp

UAG UGG
CUU Leu CCU pro CAU his CGU arg
CUC
CUA CCC CAC gln CGC
CUG CCA CAA CGA
CCG CGG
CAG
AUU İle ACU Thr AAU asn AGU ser
AUC
AUA ACC AAC lys AGC arg
AUG met ACA AAA AGA
ACG
AAG AGG
GUU Val GCU Ala GAU asp GGU gly
Include the directions of the
strands where GUC GCC GAC glu GGC appropriate.
Determine the GUA GCA GAA GGA
GUG GCG GGG
A) mRNA GAG

B) tRNA anticodons

C) amino acid sequence that will be produced.

D) Using the sequence you have and the table above, create an example of a frameshift
mutation. Just write down the pre-mutation and post-mutation codons .

29. When considering the initiation of transcription, one often finds consensus sequences
located in the region of the DNA where RNA polymerase(s) binds. Which of the
following is a common consensus sequence?
A) TATA
B) GGTTC
C) TTTTAAAA
D) any trinucleotide repeat
E) satellite DNAs

30. The gene for the DVgene (DARTVADER) is more than 2000 kb (kilobases) in length;
however, the mRNA produced by this gene is only about 14 kb long.

a. What is a likely cause of this discrepancy?

b. If you know the gene sequence, is there any way to determine the protein made from this
gene?

c. certain individuals have a mutation in this gene, which results with a 12 kb long transcript.
These individuals have a very distinctive phenotype. Can you explain why these individuals
have a 12 kb transcript instead of the 14 kb one?