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Biochemistry > Nucleic Acids and DNA Synthesis > Flashcards

Nucleic Acids and DNA Synthesis Flashcards

1
Q

Nitrogenous bases

A

Purines- adenine, guanine

Pyrimidines- cytosine, thymine

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2
Q

Aromaticity of pyrimidines/purines

A

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

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3
Q

N-glycosidic bond

A

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

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4
Q

Nucleoside vs. nucleotide

A

Nucleoside- base and sugar

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

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5
Q

Phosphodiester bond

A

Linkage between two nucleotides

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6
Q

Sugar-phosphate backbone

A

Multiple phosphodiester bonds that make up the nucleic acid

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7
Q

5’ end

A

End of the polymer with phosphate attached to C5’

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8
Q

3’ end

A

End that has a free OH group at C3’

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9
Q

Base pairing

A

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

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10
Q

Chargaff’s rules

A

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

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11
Q

Double helix

A

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

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12
Q

Z-DNA

A

Transient form in cells- line connecting phosphate zags

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13
Q

B-DNA

A

Dominates in living systems

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14
Q

A-DNA

A

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

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15
Q

Structure of RNA

A

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

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16
Q

Ribosomes

A

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

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17
Q

Prokaryotic ribosomes

A

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

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18
Q

Eukaryotic ribosomes

A

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

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19
Q

tRNA

A

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

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20
Q

Anticodon

A

Three base sequence that base pairs with mRNA

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21
Q

Denaturation

A

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

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22
Q

Tm

A

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

23
Q

Basic solutions

A

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

24
Q

DNA hybridization

A

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

25
Q

Packing of DNA

A

Supercoiled, bound to histones to form chromatin

26
Q

Histones

A

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

27
Q

Solenoid structure

A

Helical structure of several nucleosomes

28
Q

Human genome

A

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

29
Q

Proteins involved in prokaryotic replication

A

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

30
Q

oriC

A

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

31
Q

Semiconservative replication

A

After replication, one new strand and one parental strand

32
Q

Prokaryotic replication- unwinding the strands

A

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

33
Q

Prokaryotic replication- DNA strands are primed

A

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

34
Q

Prokaryotic replication- new strands synthesized

A

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

35
Q

Leading strand

A

Synthesized continuously 5’ to 3’ toward replication fork

36
Q

Lagging strand

A

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

37
Q

Differences between eukaryotes and prokaryotes

A

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

38
Q

Eukaryotic origins of replication

A

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

39
Q

Prokaryotic DNA polymerases

A

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

40
Q

Eukaryotic DNA polymerases

A

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

41
Q

Replication fork

A

Polymerase epsilon- replication of leading strand

Polymerase delta- replication of lagging strand

42
Q

Problems with linear DNA

A

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

43
Q

DNA methylation

A

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

44
Q

Damage to DNA

A

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

45
Q

Base excision repair (BER)

A

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

46
Q

Nucleotide excision repair (NER)

A

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

47
Q

Mismatched repair

A

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

48
Q

Homologous recombination

A

Crossing over of genes between homologous chromosomes

49
Q

Translocation

A

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

50
Q

Transposons

A

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

51
Q

Reverse transcriptase

A

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

52
Q

Deamination

A

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

53
Q

Equation for Tm

A

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

Biochemistry (18 decks)

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