Bio 4564/6564                       Advanced Genetics                 Spring,  2023


Test II


Name____________________                                     ID#  ______________  


Section 1.  (32 pts.)  Please circle the letters that precede the most appropriate answer(s) to the question asked.  Be aware, there is only one answer to each question.    


1.  The fidelity of DNA replication is quite astounding. During DNA synthesis, the error rate for E. coli replicase is on the order of one wrong nucleotide per


a.         10,000

b.         2.5 x 10 -8

c.         10 -9 – 10-10

d.         8 x 10-11 – 9 x 10-12

e.         one trillion


2.  The size of Okasaki fragments in eukaryotes differs slightly from those found in prokaryotes, and range around


a.               ~2,000 bps

b.               50 cM 

c.                50 bps

d.               146 bps 

e.               ~200 bps 


3.  Which of the following statements about mismatch repair of DNA is incorrect?


a.         The DNA is scanned for any base-pairing mismatches after methyl groups are added to guanines.

b.         Errors in replication made by DNA polymerase are usually corrected on the unmethylated strand of hemi-methylated dsDNA.

c.         All abnormal, non-Watson-Crick bases are always removed.

d.         Repairs from damage caused by high-energy radiation are routinely made by glycosylase

e.         Mismatch repair occurs as each strand of DNA is being replicated.


4. In the cells of prokaryotes, increased rate of methylation of specific adenines in certain sequences preferentially contributes to:


a.               an increased rate of DNA replication.

b.               a slowed rate of DNA replication.

c.                the correct separation of DNA strands.

d.               a determination of meiotically transposed DNA

e.               correcting UV induced translesions of DNA bases.


5 - 6.   In humans ______________  is an enzyme (are enzymes) that promote(s) the formation of the "D-loop" which can initiate the exchange of genetic information from one DNA strand to the other.   In contrast, ______________  is involved in resolving the Holliday junctions in prokaryotes by cleaving the Holliday junction once it is formed.


a.       Rad52

b.       RecA

c.       Rad51

d.       RuvC

e.       Spo11

f.        RecC


g.       RuvAB

h.       RuvC

i.        RecA

j.        RecB

k.       RecBCD

l.        RecC


7.             Which of the following is not found as a component of the nucleosomal core “partical”?


a.               Histone 1.1

b.               Histone 3-3

c.                Histone 4

d.               Histone 2AX

e.               Histone 2B

8.             The term “codon bias” used in the lecture refers to which of the following?


a.               The stop codon “UGA” is preferentially used to encode for tyrosine in mitochondria

b.               Some amino acids are rarely used in the proteins of some organisms

c.                In some prokaryotes the codon GUG is used for translational initiation. 

d.               In some species some codons are preferentially used to code for rare amino acids such as selenocysteine.

e.               Some codons for an amino acid are more frequently used than others and the bias often varies from

species to species  


9.             In which of the following phases of meiosis is Rad 51 believed to be most active?


a.         Metaphase

b.         Anaphase II

c.         Pachytene phase of prophase I

d.         Interphase

e.         Diakinesis phase of prophase I

f.          Diakinesis II

g.         S-phase


10.      Which type of mutation is most likely to result in the formation of a premature translational stop occurring in the expressed peptide sequence?


a.               Nonsense

b.               Missense

c.                Deleterious

d.               Insertional

e.               Reproducible


11.   Which of the following bases (?) would base pair with adenine in DNA


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In the following set of questions write in “TRUE”  ,  “FALSE”, and if you believe the answer lies somewhere in between “USUALLY” or “SOMETIMES” -when available.  If your answer is “False”, “USUALLY” or “SOMETIMES” you should briefly explain why you think so (3pts. each).


12.      Centromeres contain the very genes that encode for proteins that are required for the centromere to function.

True     /     False    /     Usually

____No proteins expressed from centromeres, themselves___________________


13.     Multiple duplications within a region of DNA invariably increase the likelihood of variation between two DNA sequences


True     /     False    /    

____What about Molecular drive ?__________________________________


14.     Silent substitutions occur 5 – 10 x more often than synonymous substitutions


True     /     False    /     Sometimes

_____Perhaps nonsynonymous, but not synonymous___________________


15.     The Ac transposon in maize has all the capabilities of a regular DNA transposon.


True     /     False    /     Usually




Section 2.  (36 pts.)  Please answer the following questions using short, concise answers. 

That being said, BE AWARE of the point distribution and give enough information to be worthy of the points allocated.


2.1 (6 pts)   How might you differentiate between “Orthologous” and “Paralogous” related genes. Give an example of each.



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2.2  (8pts) What is the function of a telomere and how is it formed?      


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2.3.  (6pts)  Differentiate between “non-replicative” and “replicative” transpositional events in prokaryotes, giving a specific example of each.


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Tn5, Tn10 Non-repicative; Tn3 Replicative





2.3.  (6pts)  Briefly discuss the function of MutS, MutL & MutH in Prokaryotes. 

What mutations do they fix and how do they work together to exert their effect.



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2.4.  (8 pts)  What are “topologically associating domains” or TADs?

Briefly discuss role of “cohesins” in their formation

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CTCF co-localizes and determines the presence at TAD boundaries of the cohesin complex,

which is also involved in establishing chromosomal interactions



2.5. (8 pts)  Briefly explain the fundamentals of DNA fingerprinting and how the DNA involved makes it possible for us to differentiate DNA source, even between immediate family members.

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Bio 4564/6564                       Advanced Genetics                 Spring,  2023


Test II


Name____________________                                     ID#  ______________  



Sections 3.  (25 pts.)  Answer one (and ONLY one) of the four questions in this section. 



3.1 (25 pts.) Single stranded/double stranded nicks and double stranded breaks provide genetic models for how different recombinatory events occurring in either prokaryotes or eukaryotes.  Discuss this statement by clearly defining the mechanism(s) by which each type of recombination may arise and what the genetic consequences of each may be.


3.2  (25 pts.)  Discuss the potential types of evolution exemplified by globin genes that were discussed in lecture (as well as any that were not (?)) and explain how such evolutionary trends can be used as classic examples for a number of characteristics of gene organization and evolutionary changes that are allowed to occur -predominantly in eukaryotes.


3.3  (25 pts.)  Transpososition and Retrotransposition are two related forms of recombination, but utilize quite distinct mechanisms to achieve recombination  in prokaryotes and eukaryotes.  Please expand upon this statement by discussing the similarities and differences between these two types of recombinatory events, using well defined examples of each.  Well labeled diagrams are more than welcome AS LONG AS THEY ARE REFERENCED IN THE TEXT OF YOUR ANSWER.


3.4  (25 pts.)  Compare and contrast the structure / function relationships of eukaryotic chromosomal DNA with prokaryotic chromosomal DNA.