Genetics Module 3 Exam

Which researchers identified DNA as the genetic material in bateriophages?

Hershey and Chase

Which researchers identified DNA as the transforming principle?

Avery, McCarty, and MacLeod

Which researchers demonstrated the phenomenon of transformation, but did not identify the transforming principle? (Base composition)

Griffith

Which researchers discovered the helical structure of DNA?

Franklin

Which researchers published the structure of DNA?

Watson and Crick

Which researcher as the first to isolate DNA?

Miescher

Which researcher determined that DNA for yeast consisted of an equal amount of purines and pryimidines?

Chargaff

Which researchers determined the DNA replication is semiconservative?

Meselson and Stahl

Which researcher determined a collinearity between DNA and protein?

Yanofsky

What is a nucleotide?

What is DNA replication?

information that is transferred from one DNA to another DNA molecule

What is transcription?

Information that is transferred from DNA to an RNA molecule

What is translation?

Information that is transferred from RNA to a protein through a code that specifies the amino acid sequence

Which one of the following is the main force stabilizing the DNA double helix?

hydrophobic interactions

During gel electrophoresis, the DNA fragments migrate toward the ___ pole.

positive

What is the structure of a purine?

What is the structure of a pyrimidine?

What is the structure of a deoxyribonucleic acid?

What is the structure of a ribonucleic acid?

What bases are purines?

Adenine and Guanine

What bases are pyrimidines?

Cytosine, Thymine, and Uracil

What distinguishes DNA from RNA?

look at the 2’ (DNA has -H and RNA has -OH)

How is DNA and RNA labelled?

1’ Carbon starts at end that connects with Nitrogen and goes around.

If you count around you can determine the 3’ and 5’ ends.

What does the backbone of DNA consists of?

deoxyribose sugars and phosphate

Find the 3’ and 5’ ends

5’ end - K

3’ end - G

Find the 3’ and 5’ ends

5’ end - J

3’ end - K

What are hydrogen bonds used for with DNA?

They are weak bonds that connect Adenine to Thymine and Cytosine to Guanine, however are not the main force of joining DNA strands

What is the main force of joining DNA strands?

Phosphodiester bonds

How many hydrogen bonds does C and G have?

3

How many hydrogen bonds does A and T have between them?

2

What gives DAN its negative charge?

phosphate group

What is the main force in stabilizing the double helix?

Hydrophobic interactions (maximized by base stacking)

Minor groove and major groove of DNA

Importance- helps determine how proteins interact with bases

Is DNA usually a right coil or a left coil?

right coil

Is the inside of DNA hydrophilic or hydrophobic?

hydrophobic

Are the backbones of DNA hydrophilic or hydrophobic?

hydrophilic

Is DNA negatively or positively charged?

negative charge

If there is 30% Adenine, calculate the % of Guanine.

30% of A = 30% of T

100% - 60% = 40% for C and G

20% for C and 20% for G

How do DNA fragments travel in gel electrophoresis?

From negative to positive poles

Which move further, smaller or larger DNA fragments?

smaller

Migration distance is _______ proportional to DNA fragment size.

inversely

How is UV light used to measure the concentration of nucleic acids?

UV light is absorbed by the ring structures in bases and absorbance is measured at 260nm

What is a hyperchromic shift?

an increase in UV absorption above 40% due to denaturation

What is Tm?

Midpoint of Thermal Denaturation

What is the relationship between melting curves, Tm, and base composition?

A higher GC content results in a higher Tm and melting point

What is a euchromatin?

lighter staining parts of the chromosome during interphase

actively transcribed genes

condenses and relaxes

What is a heterochromatin?

darker stained parts of the chromosome

contains few genes

seen in barr bodies

usually contains condensed chromatin

What is a constitutive heterochromatin?

always heterochromatin

ex: centromeres

What is a facultative heterochromatin?

can switch between heterochromatin and euchromatin

ex: barr bodies

What is a histone?

contains positively charged amino acids

bind to negatively charged DNA

What is a nucleosome?

nucleosome core + 53bp linker DNA

What makes up a nucleosome core?

8 core histones and 147 bp DNA

How to figure out the maximal number of nucleosomes that occupy a bp segment of DNA.

Nucleosome core + bp linker DNA = nucleosome

\# of bp segment of DNA / nucleosome = maximal number of nucleosomes

Which structure is 2nm?

naked DNA

Which structure is 11mn?

nucleosome fibers

What is an 11nm fiber?

tandem nucleosomes or “beads on a string”

What is supercoiling?

when DNA coils back on itself when it is overwound or underwound

What is positive supercoiling?

when DNA is over-rotated in the same direction as the DNA coil so a left-handed supercoil compensates

What is negative supercoiling?

When DNA is underwound so right handed supercoils compensate

What is the most compacted chromatin?

mitotic chromosomes

What are polytene chromosomes?

massive chromosomes produced by endopolyploidy

What is endopolyploidy?

several rounds of DNA replication without separation of replicated chromosomes

What are puffs?

areas where DNA is loosely coiled so that transcription can occur

What are bands?

band are characteristic for a strain of organism and can be used to identify specific chromosomes

What is the function of centromeres in cell division?

Centromeres contain conserved DNA sequences

What organisms have conserved DNA sequence at the centromere?

only yeast

Are centromeres heterochromatic or euchromatic?

heterochromatic

What identifies centromeres?

chromatin

What are the functions of telomeres?

provides stability for ends of chromosomes so that exonucleases do not degrade chromosomes

prevent chromosomes from joining with each other at the ends due to ligase activity

provides proper replication of the end of chromosome

What base pairs do telomeres consists mostly of and why?

C-G base pairs; more stable

What is the telomere t-loop structure?

If there is overhang of DNA sequence at the end of a chromosome, then the 3’ overhang will loop and pair with another part of the chromosome to protect the ends by proteins

How is DNA semi-conservative?

DNA replication uses an old strand as a template to direct the synthesis of a new complementary strand, resulting in a half-old/half-new double-stranded DNA molecule

What is conservative replication?

the parent molecule serves as a template for the synthesis of an entirely new molecule

What is dispersive replication?

replication that results in both original and new DNA dispersed among the two daughter strands

What is semi-conservative replication?

each of the daughter molecules have one old strand from the parent molecule and one new strand

What is theta replication?

Circular DNA

No breakage of nucleotide strand

1 replicon (origin)

unidirectional or bidirectional

product- two circular molecules

What is theta replication common in?

bacteria and other circular DNA molecules

What is rolling circle replication common in?

the F factor and viruses

What is rolling circle replication?

circular DNA

involves breakage of nucleotide strand

only one replicon (origin)

unidirectional

product- one circular molecule and one linear molecule that may circularize

What is linear eukaryotic replication?

linear DNA

no breakage of nucleotide strand

multiple replicons

bidirectional

two linear molecules

Importance of DNA polymerase III

responsible for most DNA synthesis

proofreads with 3’-5’ exonuclease activity

proofreads with 5’-3’ polymerase activity

What is the importance of DNA polymerase I?

5’-3’ exonuclease activity to remove RNA primers

proofreads with 3’-5’ exonuclease activity

proofreads with 5’-3’ polymerase activity

What is the role of DNA poly II?

DNA repair and to restart replication after damaged DNA halts synthesis

What is the role of DNA poly IV?

DNA repair

Why are conditional mutations necessary to study the function of various genes involved in DNA replication?

Conditional mutants allow normal phenotypes under normal condition to display an altered function, allowing researchers to observe changes in the phenotype.

Identify the following:

1. Gyrase
2. Parental strand
3. RNA primer
4. Lagging strand template
5. RNA primase
6. DNA Poly III
7. Okazaki fragment
8. Lagging strand
9. DNA Poly I
10. Ligase
11. Helicase
12. Single-strand Binding Protein
13. DNA Poly III
14. Lagging strand template
15. Leading strand
16. Leading strand
17. Lagging strand
18. Continuous synthesis

Identify the following:

A - Ligase

B - DNA Poly I

C - Lagging strand DNA poly III

D- ?

E - Leading strand DNA Poly III

F - Single-strand binding protein

G - Primase

H - Helicase

I - Gyrase

Determine which end is the leading strand and which end is the lagging strand, as well as the direction of the replication fork.

Leading strand - lower strand

Lagging strand - higher strand

Replication fork - right

What is the function of ligase?

to connect Okazaki fragments by sealing nicks in the sugar-phosphate backbone

What is the function of primase?

the create a short RNA primer for the DNA ploymerase

What is the of helicase?

unwinds the DNA double helix

What is the function of gyrase?

relieves tension due to supercoils caused by strand separation

What is the function of single stranded binding proteins?

binds to the strands of DNA to keep them separated

Is lagging strand or leading strand continuous synthesis?

leading strand

How does eukaryotic replication differ from prokaryotes?

there are many origins of replication

the origin must be licensed for replication to occur

linear chromosomes

lots of different DNA poly molecules with various roles

have telomeres to replicate

nucleosome assembly immediately follows replication

Which 3 proteins are responsible for the unwinding of DNA?

helicase

Single-stranded binding protein

gyrase

What proteins make up primosome?

helicase and primase

Why is replication of the end of linear chromosomes problematic?

In the absence of special mechanisms, DNA replication would leave gaps at the end of the chromosome, and the chromosome would shorten each time the cell divides

How does telomerase accomplish replication of telomeres?

Telomerase contains RNA which is used to make several repeats of DNA, extending the 3’ end. The RNA is used as a template for DNA synthesis and after several nucleotides are added, telomerase moves along the DNA and is eventually removed.

(Telomerase extends DNA which fills in the gap due to the removal of RNA primer)

What is a ribonucleoprotein made of?

RNA and proteins