Nucleic Acids and DNA Synthesis

Question 1

Nitrogenous bases

Answer 1

Purines- adenine, guanine

Pyrimidines- cytosine, thymine

Question 2

Aromaticity of pyrimidines/purines

Answer 2

Can convert between the lactam and lactim forms, lactam (keto) form dominates at physiological pH

Question 3

N-glycosidic bond

Answer 3

Bond between the base and the sugar, normally in the anti conformation

Question 4

Nucleoside vs. nucleotide

Answer 4

Nucleoside- base and sugar

Nucleotide- includes the base, sugar, and phosphate(s)

Question 5

Phosphodiester bond

Answer 5

Linkage between two nucleotides

Question 6

Sugar-phosphate backbone

Answer 6

Multiple phosphodiester bonds that make up the nucleic acid

Question 7

5’ end

Answer 7

End of the polymer with phosphate attached to C5’

Question 8

3’ end

Answer 8

End that has a free OH group at C3’

Question 9

Base pairing

Answer 9

DNA contains two polynucleotide strands that base pair through hydrogen bonds, each contains one purine and one pyrimidine

Question 10

Chargaff’s rules

Answer 10

[A] = [T], [G] = [C], purines = pyrimidines

Question 11

Double helix

Answer 11

Two antiparallel strands base pair together are twisted to form double helix

Question 12

Z-DNA

Answer 12

Transient form in cells- line connecting phosphate zags

Question 13

B-DNA

Answer 13

Dominates in living systems

Question 14

A-DNA

Answer 14

Dominates in DNA-RNA hybrids, tightly wrapped, dehydrated form of B-DNA

Question 15

Structure of RNA

Answer 15

RNA has many forms, structure related to function, typically single stranded, has secondary structure, similar to DNA structure

Question 16

Ribosomes

Answer 16

Site of protein synthesis in the cell, contains large and small subunits, comprised of protein and RNA, rRNA is important to ribosome function

Question 17

Prokaryotic ribosomes

Answer 17

Total size 70S- 50S + 30S, three types of rRNA, 23, 16, 5S

Question 18

Eukaryotic ribosomes

Answer 18

Total size 80S- 60S + 40S, four types of rRNA, 28, 18, 5.8, and 5S, mitochondrial ribosomes- 55S, similar to prokaryotes

Question 19

tRNA

Answer 19

tRNA secondary structure is important in protein synthesis, anticodon loop is responsible for recognizing the codon on the mRNA, tRNA bring in the amino acid being added to the polypeptide

Question 20

Anticodon

Answer 20

Three base sequence that base pairs with mRNA

Question 21

Denaturation

Answer 21

Separation of the double helix into two separate strands, heat can disrupt hydrogen bonds and cause DNA denature, basic solutions denature DNA and RNA

Question 22

Tm

Answer 22

Temperature where 50% of DNA is denatured, determined by the amount of G:C vs. A:T, changed by salt concentration (stabilizes the solution)

Question 23

Basic solutions

Answer 23

Denatures DNA, causes RNA to break apart because the OH group on ribose loses its proton, negative charged oxygen breaks phosphodiester bond

Question 24

DNA hybridization

Answer 24

DNA can be hybridized to a complementary strand of RNA, temperature reduced slowly

Question 25

Packing of DNA

Answer 25

Supercoiled, bound to histones to form chromatin

Question 26

Histones

Answer 26

Major protein that forms chromatin, high percentage of lysine and arginine (positively charged), H2A, H2B, H3, and H4 form nucleosome, H1 joins nucleosomes together

Question 27

Solenoid structure

Answer 27

Helical structure of several nucleosomes

Question 28

Human genome

Answer 28

Humans have 23 pairs of chromosomes (22 somatic, 1 sex), genes are arranged across each chromosome

Question 29

Proteins involved in prokaryotic replication

Answer 29

Helicase, topoisomerase, gyrase, single-strand binding proteins, DNA polymerase (I, II, III), primase, DNA ligase

Question 30

oriC

Answer 30

Sequence in the prokaryotic genome where replication is initiated- DnaA binds and helix unwraps, two replication forks

Question 31

Semiconservative replication

Answer 31

After replication, one new strand and one parental strand

Question 32

Prokaryotic replication- unwinding the strands

Answer 32

Helicase unwinds the DNA strands, topoisomerase breaks/rejoins phosphodiester bonds to relieve supercoiling, single-strand binding proteins bind to DNA as it unwinds to prevent re-associating and enzyme degradation

Question 33

Prokaryotic replication- DNA strands are primed

Answer 33

Primase adds RNA primers to DNA (DNA polymerase needs 3' OH), after DNA is synthesized the primers are removed by RNase H and DNA pol I

Question 34

Prokaryotic replication- new strands synthesized

Answer 34

DNA polymerase III adds the next deoxyribonucleotide making a new strand 5' to 3', proof reads as it functions, produces leading and lagging strands

Question 35

Leading strand

Answer 35

Synthesized continuously 5' to 3' toward replication fork

Question 36

Lagging strand

Answer 36

Synthesized discontinuously 5' to 3' away from the replication fork, produces Okazaki fragments that are joined by DNA ligase

Question 37

Differences between eukaryotes and prokaryotes

Answer 37

Eukaryotes have larger genomes, histones/nucleosomes, prokaryotic circular DNA

Question 38

Eukaryotic origins of replication

Answer 38

Have multiple origins of replication, each origin has two replication forks, fork from one origin will meet replication fork from another, multiple origins makes it possible to copy complex genome

Question 39

Prokaryotic DNA polymerases

Answer 39

Polymerase I- replication, repair, primer excision Polymerase II- DNA repair Polymerase III- major replication polymerase, 3'-5' exonuclease for proofreading

Question 40

Eukaryotic DNA polymerases

Answer 40

Polymerase alpha- associated with primase Polymerase beta- DNA repair, primer excision Polymerase gamma- mitochondrial DNA synthesis Polymerase delta- replication, 3'-5' exonuclease for proofreading Polymerase epsilon- replication, 3'-5' exonuclease for proofreading, DNA repair

Question 41

Replication fork

Answer 41

Polymerase epsilon- replication of leading strand | Polymerase delta- replication of lagging strand

Question 42

Problems with linear DNA

Answer 42

DNA polymerase cannot copy the end of the lagging strand, produces a 3' overhang, telomerase adds nucleotides to the 3' end but still have overhang

Question 43

DNA methylation

Answer 43

DNA can be methylated after replication, adenine and cytosine, species specific, methyl groups project into groove and are bound by DNA binding proteins

Question 44

Damage to DNA

Answer 44

DNA is exposed to chemical and physical agents that can damage it daily- smoking (benzopyrene), sun exposure (thymine dimer), x-ray (hydroxyl radical), deamination, translation-coupled repair

Question 45

Base excision repair (BER)

Answer 45

Removal of a damaged base that cannot be directly repaired, glycosylase cleaves glycosidic bond, deoxyribose is cleaved by an AP endonuclease, residues are removed by an exonuclease, DNA polymerase fills the gap, DNA ligase seals the nicks

Question 46

Nucleotide excision repair (NER)

Answer 46

Corrects large segments such as pyrimidine dimer or lesions with bulky substituents, endonuclease cleaves distorted regions and removes DNA segment, DNA polymerase fills the gap and DNA ligase seals the nicks

Question 47

Mismatched repair

Answer 47

Function to fix errors in replication that are missed by proofreading, methyltransferase has not had time to methylate newly synthesized strand, determines which base is an error, steps similar to BER and NER

Question 48

Homologous recombination

Answer 48

Crossing over of genes between homologous chromosomes

Question 49

Translocation

Answer 49

Caused by breaks in two nonhomologous chromosomes, balanced translocation results in no loss of genetic function because the cut occurs between genes, unbalanced results in extra or missing genes

Question 50

Transposons

Answer 50

Sequences of DNA that are moved from place to place in the genome, end of the transposon has inverted repeats that act as target sequence, staggered cuts produce single stranded ends that are ligated to the transposon

Question 51

Reverse transcriptase

Answer 51

Makes DNA from RNA, known as cDNA, can be incorporated into the human genome, causes disease

Question 52

Deamination

Answer 52

Cytosine loses the amino group and becomes uracil, can become thymine if methylated, disrupts base pairing and can permanently change DNA sequence, if DNA had uracil than deamination would be highly mutagenic

Question 53

Equation for Tm

Answer 53

Tm (deg C) = 69.3 + 0.41 (%G + C)