DNA/RNA

Question 1

3 main classes of RNA species in human cells

Answer 1

1. structural
2. information carrying
3. regulatory

Question 2

structural RNA

Answer 2

1. ribosomal RNA (rRNA)
2. transfer RNA (tRNA)
3. small nuclear RNA (snRNA)
4. small nucleolar RNA (snoRNA)

Question 3

regulatory RNA

Answer 3

1. micro RNA (miRNA)

2. small interfering RNA (siRNA)

Question 4

information containing RNA

Answer 4

messenger RNA (mRNA)

Question 5

purine

Answer 5

adenine
guanine
double ring

Question 6

pyrimidine

Answer 6

cytosine
thymine
uracil
single ring

Question 7

central dogma

Answer 7

DNA–> replication–>DNA
DNA–> transcription–>RNA
RNA–>translation–> protein

Question 8

building blocks of nucleic acids

Answer 8

ribonucleiotide and 2’deoxy-nucleotide residues

Question 9

universal energy currency is

Answer 9

ATP

Question 10

building block of RNA

Answer 10

ATP

Question 11

Nucleotides are NOT in

Answer 11

DNA and RNA

Question 12

ribose is a

Answer 12

5 carbon sugar thats the primary building block of ribonucleic acids
it is a deoxyribose that has been de-hydroxylated at the 2’ position

Question 13

nucleosides are

Answer 13

the central ribose sugr and bas attached to it at the 1’ position

Question 14

a nucleoside with one phosphate group attached tot eh 5’ position of the ribose is called

Answer 14

nucleotide or nucleoside monophosphate

Question 15

if there is a chain of two phosphates tagged on 5’ position, it is a

Answer 15

nucleoside diphosphate

tri if it’s 3…

Question 16

phosphates are fairly hydro_____, while bases are

Answer 16

hydrophillic

hydrophobic

Question 17

diseases that can result from accumulation of excess purine derivatives in tissue

Answer 17

gout: build up of uric acid in joints as precipitant of purines

Lesch-Nyhan Disease: causes severe neuro symptoms

Question 18

3’ end

Answer 18

open hydroxyl group at that ribose position

Question 19

5’ end

Answer 19

phosphate end

Question 20

phosphodiester link is between

Answer 20

the phosphate and hydroxyl group of 3’ to 5’ end

Question 21

which is more soluble, a purine or pyrimidine?

Answer 21

a purine is less soluble

Question 22

solubility:

nucleoside, base, nucleotide

Answer 22

nucleotide> nucleoside> base

Question 23

conventional way of writing DNA

Answer 23

5’ –> 3’

Question 24

DDL and AZT drugs work by

Answer 24

inhibiting DNA synthesis by the reverse of transcriptase (RNA–>DNA), hence inhibiting HIV replication

Question 25

Avery, McCloud, McCarty discovered

Answer 25

DNA is genetic material

the mouse thing

Question 26

Franklin and Wilkins

Answer 26

x ray diffraction of moist DNA fibers showed helical structure with 10 layer line and major repeat of 3.4 nm

Question 27

watson and crick

Answer 27

double helical structure with major and minor groove

Question 28

chargaff’s rule

Answer 28

1. molar ratios of total purine and total pyrimidines are roughly equal (G+A= C+T)
2. the molar rations of adenine to thymine and guanine to cytosine are equal
   (G=C, A=T)

Question 29

why is DNA so much more stable than RNA?

Answer 29

2’ hydroxyl group on ribose makes it much less stable

Question 30

why does DNA grow 3’ to 5’?

Answer 30

the 3’ OH group of the 5” end attacks the next 5’ a-phosphate

Question 31

G-C have ___ H- bonds

Answer 31

3

Question 32

A-T have ____ H bonds

Answer 32

2

Question 33

What factors affect the melting point of DNA?

Answer 33

Factors affecting the Tm or DNA:
• Salt concentration: high salt concentrations will increase the Tm
o When salt concentration decreases, the negatively charged phosphate groups on the phosphodiester backbone are no longer stabilized by positively charged ions.
o The negative charge of the backbone tends to force the strands apart
o Thus, higher salt concentrations neutralized this repulsion and increase DNA stability
• Extremes of pH will alter the ionization states of the groups on the bases which provide/accept H-bonds
• Increase in DNA chain length will increase Tm
• Increase in G=C base pairs will increase Tm
o G=C has 3 H-bonds, while A-T has only 2 H-bonds.

Question 34

Covalent methylation of human DNA:

Answer 34

Covalent methylation of human DNA: addition of a methyl group to the 5 position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring
o Major covalent modification of human DNA in which a methyl group is attached to a Cytosine
o CpG sites: regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length. “CpG” is shorthand for “—C—phosphate—G”
o Aka cytosine and guanine separated by a phosphate
o “CpG” notation is used to distinguish this linear sequence from the base-pairing of cytosine and guanine
o CpG islands: regions of DNA with higher concentrations of CpG sites, often associated with the “start” site of a gene (promoter or promoter proximal element)
o Basis of “epigenetics”
o Also important for cancers: hypermethylation in silencing tumor suppressor genes, hypomethylation in aberrant transcription of oncogenes

Question 35

Deamination of bases is a cause of

Answer 35

of mutations
o Removal of an amine group
o Deamination of cytosine converts it to uracil
o Easily recognized and repaired because Uracil is so obviously not supposed to be a part of DNA
o Deamination of 5-methyl cytosine converts it to thymine
o Most common mutation, not recognized by the repair machinery so often persists
o Cause of rarity of CpG sites in eukaryotic cells
o Deamination of Guanine results in the formation of xanthine
o Selectively base pairs with thymine instead of cytosine
o Results in a post-replicative transition mutation, where the original G-C base pair transforms into an A-T base pair
o Correction of this mutation involves the use of alkyladenine glycosylase during base excision repair
o Deamination of Adenine results in the formation of hypoxanthine
o Selectively base pairs with cytosine instead of thymine
o Results in a post-replicative transition mutation, where the original A-T base pair transforms into a G-C base pair

Question 36

Depurination

Answer 36

. Depurination also results in mutations
o The purine base (adenine or guanine) is removed from the deoxyribose sugar by hydrolysis of the beta-N-glycosidic link between them
o After depurination, the sugar phosphate backbone remains and the sugar ring has a hydroxyl (-OH) group in the place of the purine – apurinic site
o Depurinated bases in double-stranded DNA are efficiently repaired by portions of the base excision repair pathway
o Depurinated bases in single-stranded DNA undergoing replication can lead to mutations, because in the absence of information from the complementary strand, BER can add an incorrect base at the apurinic site, resulting in either a transition or transversion mutation

Question 37

Ultraviolet light covalently links

Answer 37

. Ultraviolet light covalently links thymines: pyrimidine dimmers
o Creates a kink in the DNA
o Dimers may be repaired by photoreactivation or nucleotide excision repair, but unrepaired dimers are mutagenic
o In humans they are the primary cause of melanomas

Question 38

. Alkylating agents are carcinogenic

Answer 38

. Alkylating agents are carcinogenic
• Alkylation = transfer of an alkyl group from one molecule to another
• Nucleophilic groups are reactive to alkylating agents

Question 39

Explain the chemistry of DNA polymerization and how nucleoside analogues are used as drugs.

Answer 39

In DNA polymerization, new bases are added to the growing strand via the nucleophilic attack of the 3’ Hydroxyl of the 5’end on the alpha phosphate on the 5’ carbon of the new base.

Nucleoside analogues are engineered to be antiviral drugs that halt viral DNA replication.

Instead of a free hydroxyl group on the 3’ carbon, they have an Azide (N=N=N) or a hydrogen atom. When incorporated into the growing DNA strand, there is no longer a free 3’ hydroxyl to act as a nucleophile and add bases to the growing chain. As a result, replication stops.