Unit 3.2 (dna)

Question 1

What kind of bases have strong UV absorbance? At what frequency does this occur?

Answer 1

Purines all have strong UV absorbance (max ~260 nm)

Question 2

What is a Nucleoside?

Answer 2

Nitrogenous Base + Sugar
Sugar = 2’-deoxy-D-ribose
Bond = B-N-glycosidic bond

Question 3

What is a nucleotide?

Answer 3

Nucleoside + Phosphate
By default, phosphate group is on the 5’OH group (can also be on 3’ C)

Question 4

What is cAMP? Why is it important?

Answer 4

Derived from ATP
cAMP is used in many biological process in intracellular signaling as an important 2nd messenger

Question 5

What is Zidovudine?

Answer 5

Many antivirals are nucleoside/nucleotide analogs
Zidovudine is a nucleoside analog reverse transcriptase inhibitor used to treat HIV

Question 6

What is Emtricitabine?

Answer 6

Another antiviral medication that is also used for the treatment of HIV infection for adults and children

Question 7

What are minor bases?

Answer 7

RNA, particularly tRNA, contains minor bases
In DNA, these are usually methylated forms of the major bases (usually have roles in regulation or in protecting genetic information

Question 8

What makes Inosine significant?

Answer 8

Inosine is commonly found in tRNAs essential for wobble base pairs

Question 9

Describe the structure of the two classes of polynucleotides

Answer 9

Nucleotides joined by phosphodiester linkages
RNA = Ribonucleic acid (2’ OH) (Uracil)
DNA = Deoxyribonucleic acid (2’ H) (Thymine)

Question 10

Describe the primary structure of DNA/RNA

Answer 10

Sequence of nucleotides
Read from the 5’ end to the 3’ end

Question 11

What is the biggest difference between DNA and RNA? (RNA’s problem)

Answer 11

Stability!
RNA is susceptible to base catalyzed hydrolysis (due to presence of 2’ OH)

Question 12

What are Chargaff’s rules?

Answer 12

Explains base ratios in DNA
#G = #C
#A = #T

Question 13

Who solved 2° structure of DNA? What is the 2° structure?

Answer 13

Watson and Crick
The Double Helix

Question 14

Whose data was important for Watson and Crick to determine the secondary structure of DNA? (they stole it)

Answer 14

Rosalind Franklin’s X-ray fiber diffraction data was crucial (also used Erwin Chargaff’s rules)

Question 15

What simple principle is DNA replication based on?

Answer 15

Complementarity!

Question 16

Describe the central dogma of molecular biology

Answer 16

Question 17

Describe B DNA structure. What kind of helix does it have? Where are the bases relative to helix? Describe the major and minor grooves. Where are the phosphate backbones located? What is the pitch? How many bases per turn? What is the helix rise?

Answer 17

Question 18

In what direction do the two chains run in a B DNA helix?

Answer 18

The two chains are antiparallel

Question 19

Describe the difference between syn- and anti- conformations in nucleotide sugars in DNA/RNA

Answer 19

Question 20

What handedness is A DNA? Describe its major and minor groove. What kind of molecules assume an A DNA structure?

Answer 20

Right handed
Major Groove: Narrow and Deep
Minor Groove: Wide and Shallow
RNA-RNA/RNA-DNA hybrids assume A-DNA structure
“Dried out DNA” (75% vs 92% humidity)

Question 21

What is the naturally occurring form of DNA?

Answer 21

B DNA

Question 22

What handedness is Z-DNA? Describe is major and minor grooves. Where does this form of DNA occur?

Answer 22

Left Handed
Major Groove: Flat
Minor Groove: Narrow and Deep
Occurs in alternating purine-pyrimidine tracts (favored in high salt conc.)

Question 23

What are Telomeres? What are they rich in?

Answer 23

Ends of Linear Chromosomes (keep them from unravelling)
Guanidine-rich regions

Question 24

Describe the general structure of RNA

Answer 24

Most (but not all) RNA is single-stranded
Has “wound back” double helical regions that assume A type helix

Question 25

What are two common patterns of RNA 3° structure?

Answer 25

Question 26

What kind of enzymes affect DNA supercoiling (2 types)

Answer 26

Question 27

What are topoisomerase inhibitors widely used as? What is a specific drug example of this?

Answer 27

Anticancer and antibacterial agents

Question 28

Why is DNA packaging important?

Answer 28

DNA in each cell is 1.1m long!

Question 29

How is Prokaryotic DNA packaged?

Answer 29

Supercoiled circular DNA is bound to small, basic proteins to give bacterial chromosomes in the nucleoid

Question 30

What are bacterial plasmids?

Answer 30

SEPERATE small, circular molecules that carry genes for their own replication and often code for beneficial enzymes

Question 31

How is Eukaryotic DNA packaged?

Answer 31

Chromatin/chromosomes (depending on stage of mitosis)
DNA is coiled around histone octamer (2x histones H2A, H2B, H3, H4) called a NUCLEOSOME (look like beads on a string)

Question 32

How much DNA is wrapped around the nucleosome

Answer 32

1.8 turns of DNA is wrapped around each nucleosome

Question 33

What unique property of histones allows them to effectively bind to DNA?

Answer 33

Histones are relatively small proteins rich in the basic amino acids Lysine and Argine, whose side chains have a positive (+) charge (DNA is negative)

Question 34

What is unique about Histone H1?

Answer 34

Not involved in nucleosome… binds DNA in between nucleosomes!!!

Question 35

What is unique about Mitochondrial and Chloroplast DNA?

Answer 35

Circular DNA devoid of histones that replicate on their own

Question 36

What are 3 common types of DNA damage? What do they cause?

Answer 36

(1) UV-radiation - Causes thymine dimers (affects structure of DNA, which leads to mutation, which leads to cancer)
(2) Alkylation - Causes DNA mismatch mutations that can lead to cancer
(3) HNO2 (from processed food) causes DNA mismatch mutations that lead to cancer