DNA/RNA LO

Question 1

What are the purines?

Answer 1

adenine, guanine (PURe As Gold)

Question 2

what are the pyrimidines?

Answer 2

cytosine, thymine, and uracil

Question 3

what is ribose?

Answer 3

5 carbon sugar that is the primary building block of ribonucleic acids

Question 4

how is deoxyribose different than ribose?

Answer 4

deoxyribose has been dehydroxylated at the 2’ position

Question 5

what is a nucleoside?

Answer 5

central ribose sugar and a base attached to it at the 1’ position

Question 6

what is a nucleotide?

Answer 6

a nucleoside with at least one phosphate group attached to the 5’ position of the ribose

Question 7

what is the universal energy currency in the body?

Answer 7

ATP

Question 8

what is the solubility relationship between pyrimidines and purines?

Answer 8

pyrimidine > purine

in regards to solubility

Question 9

what is the solubility relationship between nucleosides, bases, and nucleotides?

Answer 9

nucleotide > nucleoside > bases

in regards to solubility

Question 10

between bases and nucleosides, which is less soluble?

Answer 10

base is less soluble than nucleoside

Question 11

Gout is caused by the build up of ________ which is a precipitant of _______

Answer 11

uric acid, purines

Question 12

The low solubility of purines and their accumulation leads to which 2 diseases covered in lecture?

Answer 12

Lesch-Nyhan disease and gout

Question 13

in regards to the deoxyribose, why is the direction 5’ to 3’ polarity?

Answer 13

5’ end has phosphate and 3’ end has hydroxyl group. phosphate at the 5’ end will bind with the hydroxyl group at the 3’ end

Question 14

What did the Avery, McCloud, and McCarty experiment find?

Answer 14

established DNA as the genetic material with their pneumococcus experiments. (smooth strain killed mice, rough strain did not. DNA from heat killed S cultured with R then killed mice BAM!)

Question 15

what did the Franklin and Wilkins find and how?

Answer 15

helical structure of DNA through x-ray diffraction

Question 16

what are Watson and Crick known for?

Answer 16

definitive double-helical structure

Question 17

What are Chargaff’s rules?

Answer 17

1. Molar ratios of total purines and total pyrimidines are roughly equal (G+A = C+T)
2. the molar ratios of adenine to thymine, and guanine to cytosine are roughly equal (G=C, A=T)
3. G+C / A+T ratio is different for different organisms

Question 18

Describe the Watson-Crick model for DNA structure

Answer 18

2 strands in right handed helix
sugar/phosphate groups on the outside of helix (hydrophilic)
bases paired and stacked on the inside (hydrophobic)
major groove and minor groove
10 bp per turn of helix
horizontal distance covered by A-T is almost identical to G-C

Question 19

what 3 factors within the double helix help stabilize the electrostatic repulsion of the phosphate groups?

Answer 19

1. neutralized by positively charged species in cell (magnesium)
2. base pair linkages provide stability
3. base pairs stack on top of one another which allows for delocalization of electrons

Question 20

what does increasing the salt concentration do to the stability of the DNA?

Answer 20

increases the stability of DNA

Question 21

what do extreme pH do to the stability of the DNA?

Answer 21

decreases the stability through altering the ionization of the bases which form H-bonds

Question 22

what does increasing the length of the DNA strand do to the stability?

Answer 22

increases stability

Question 23

what does a higher GC content do to the stability of the DNA?

Answer 23

increases stability

Question 24

where is circular DNA found?

Answer 24

prokaryotes and mitochondra

Question 25

What occurs during methylation of base pairs?

Answer 25

methyl group is added to cytosine or adenine DNA nucleotides

Question 26

what are the consequences of DNA methylation?

Answer 26

decreases gene activity and there is abnormal gene regulation

Question 27

what is the major covalent modifcation of human DNA?

Answer 27

methylation of C at CpG sequences

Question 28

when does methylation of cytosine mostly occur?

Answer 28

when cytosine is adjacent to a guanine

Question 29

what does deamination of methylcytosine yield?

Answer 29

thymine

Question 30

why is deamination of methylcytosine a serious problem?

Answer 30

because turns into thymine, then on replication, an adenine will be added instead of a guanine

Question 31

what compound can increase the speed of deamination and where is it mostly found?

Answer 31

nitrous acid, cigarette smoke

Question 32

what becomes sensitive to breakage after depurination?

Answer 32

phosphate backbone

Question 33

what happens during depurination?

Answer 33

breaking off purine base from ribose and leaving a hydroxyl group

Question 34

what can happen if you have a few depurinations right next to each other on DNA?

Answer 34

breakage of the phosphate backbone

Question 35

what is usually created as a result of UV radiation in DNA?

Answer 35

thymine dimers

Question 36

how are thymine dimers usually repaired?

Answer 36

nucleotide excision repair

Question 37

what type of agents are considered carcinogens?

Answer 37

alkylating agents (mustard gas, dimethylsulfate, dimethylnitrosamine, CISPLATIN (cancer drug))

Question 38

through what process does actinomycin D work?

Answer 38

intercalation. Molecule intercalates into the DNA and then replication cannot continue

Question 39

why can intercalation cause cancer cells to enter apoptosis?

Answer 39

causes kink in DNA and replication cannot occur, therefore cell recognizes that it is not functioning properly

Question 40

what does topoisomerase do?

Answer 40

removes knots of DNA by removing supercoils

Question 41

what is underwound DNA?

Answer 41

produces negative supercoils and decreased twist

Question 42

what is overwound DNA?

Answer 42

produces positive supercoils and increased twist

Question 43

what are the 4 methods of attacking DNA metabolism?

Answer 43

1. syntehsis of precursors (dNTP) 2. intercalation (getting in the middle) 3. covalently binding bps 4. disrupting topoisomerases

Question 44

what are the 3 main types of RNA in a human cell?

Answer 44

1. structural 2. regulatory 3. information-containing

Question 45

what is the function of rRNA?

Answer 45

(ribosomal RNA) make up functional units of ribosomes and translate mRNA

Question 46

what is the function of tRNA?

Answer 46

(transfer RNA) brings amino acid specified by codon to ribosome

Question 47

what is the function of snRNA and siRNA?

Answer 47

(small nuclear RNA and small interfering RNA) function with in-cell modifications such as splicing

Question 48

what is the function of miRNA and siRNA?

Answer 48

(micro RNA and small interfering RNA) downregulate gene expression

Question 49

which is more easily hydrolyzed when comparing RNA and DNA?

Answer 49

RNA

Question 50

why is RNA more easily hydrolyzed than DNA?

Answer 50

there can be a nucleophilic attack by 2' OH on the phosphodiester bond

Question 51

what is the ease of hydrolyzing RNA important for?

Answer 51

changes in gene expression

Question 52

what is the usually the final form of RNA in humans after it is produced?

Answer 52

single strand RNA

Question 53

why can RNA produce many different conformations?

Answer 53

there is rotation around the bonds, not hindered by hydrogen bonds from another strand like in DNA

Question 54

How does puromycin work?

Answer 54

nucleotide analogue that mimics tRNA acceptor region. therefore allows peptide transfer and termination of translation

Question 55

where do most bacteria get their antibiotic resistance from?

Answer 55

environmental DNA such as plasmids

Question 56

how does RNA form hairpin loops?

Answer 56

AU, GC, and GU base pairs

Question 57

what does E site of ribosomes hold?

Answer 57

holds RNA that will exit

Question 58

what does the P site of ribosomes hold?

Answer 58

holds tRNA with growing polypeptide attached

Question 59

what does the A site of ribosomes hold?

Answer 59

holds the aminoacyl tRNA

Question 60

what happens at the active site of a ribosome?

Answer 60

location where polypeptide chain is formed

Question 61

what are the 4 types of structural RNA?

Answer 61

1. rRNA 2. tRNA 3. snRNA 4. snoRNA

Question 62

what are the 2 types of regulatory RNA's?

Answer 62

1. miRNA | 2. siRNA

Question 63

which RNA is information containing?

Answer 63

mRNA

Question 64

how is nucleic acid melting and annealing used to detect one specific DNA sequence in total cellular DNA?

Answer 64

you break the hydrogen bonds between the 2 strands of DNA thus pulling the 2 strands apart. After the DNA is in single strand form it wants to re-anneal with it's complement. If you have a primer in the solution, you can measure if a certain patient has DNA specific to the primer or specific target that you are interested in.