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Biochemistry I > Exam 3 > Flashcards

Exam 3 Flashcards

Lecture 14, 15, and 16

1
Q

What are the 5 types of spontaneous DNA damages?

A

replication errors, replication failures, oxidation, base loss, and deamination

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2
Q

What are the 2 types of induced DNA damages?

A

chemical and radiation

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3
Q

What are mutagens?

A

specific chemical agents that alter base sequences

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4
Q

What do transition mutations do or connect?

A

(pyrimidine-to-pyrimidine and purine-to-purine)

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5
Q

What do transversions mutations do or connect?

A

(pyrimidine-purine and purine-to-pyrimidine)

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6
Q

What is a frameshift?

A

Insertions and deletions (a nucleotide or a small number of nucleotides)= change in the reading frame
Ex: for a base pair addition, it completely alters the following codons and polypeptides

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7
Q

How can DNA be damaged? (4)

A

Mismatched bases
–Polymerase error rate about 1 in 104=Fidelity of polymerase
–Deamination of C to U leading to mismatch
Missing bases.
Structural damage = Dimer formation.
Broken phosphodiester bonds. Chemicals/radiation

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8
Q

What are the 4 things that alter specific bases?

A

Oxidizing Agents
Deamination
Alkylating Agents
UV Light/radiation

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9
Q

What is an example of an oxidizing agent?

A

Guanine gets oxidized to 8-oxoguanine which leads to the pairing to A instead of the original C

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10
Q

What do oxidizing agents do?

A

They oxidize the bases and make them form with the incorrect base. They take an —H away and put a C=O in its place (carbonyl)

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11
Q

Explain Deamination

A

Hydrolyizes (H2O added) making the NH2 group change to a C=O group on the base. This makes it bind to the incorrect base. This carbonyl group makes it easier for this new compound to bond with H’s

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12
Q

Explain what alkylating agents do

A

Bases react with the hydrocarbons in an “alkylation reaction”. Ex: Aflatoxin is converted into a highly reactive epoxide that reacts with guanine forming a compound that, during replication, converts a G-C base pair into a A-T base pair.

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13
Q

Explain what UV light and radiation does

A

This is described as forming Thymine dimers on the same DNA strand

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14
Q

What are the 5 DNA repair pathways we have to know for Prokaryotes?

A
  • Mismatch repair: Mut S, L, and H
  • Direct enzymatic repair-thymidine dimers
  • Base excision repair- AP endonuclease
  • Nucleotide Excision Repair-UVR A, B, and C
  • Double stranded break repair: Recombination (next lecture)
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15
Q

Explain how mismatch repair works

A

A G-T mismatch is recognized by MutS. MutL then binds to MutS and activates the MutH nuclease. The MutH then cleaves the backbone in the vicinity of the mismatch. A segment of the DNA strand containing the error T is removed by exonuclease 1 and synthesized anew by DNA poly 3.

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16
Q

Explain how the Direct Enzymatic Repair works

A

This is done without having to remove any fragments of DNA. An example would be the photochemical cleavage of pyrimidine dimers by a photo-reactivating enzyme called “DNA photolyase”. The E coli enzyme using light energy (300 to 500 nm of light) and transfers this energy to FADH which then transfers energy to break the dimer. The resulting pyrimidine anion reduces FADH and the repaired DNA is released.

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17
Q

Nuclease can cleave at the 3’ or 5’ of a phosphodiester bond:
If it cleaves at 3’, it yields _____ -PO4 and _____-OH which then is called ___exo/endonuclease
If it cleaves at 5’, it yields ___-PO4 and ___-OH which then is called ___exo/endonuclease

A

If it cleaves at 3’, it yields __5’___ -PO4 and __3’___-OH which then is called 3’exo/endonuclease

If it cleaves at 5’, it yields __3’_-PO4 and _5’__-OH which then is called 5’exo/endonuclease

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18
Q

Explain how does Base excision repair (BER) work

A

An example of this would be AlkA which is an enzyme, binds to the damaged DNA which flips the affected base out of the DNA double helix and in the the active site of the enzyme. The enzyme then acts as a glycosylase which cleaves the glycosidic bond to release the damaged base. At this stage, the backbone of the DNA is intact but a base is missing. The hole is called an AP site b/c it is apurinic (devoid of A or G) or apyrimidinic (devoid of C or T). An AP endonuclease recognizes this defect and nicks the backbone adjacent to the missing base. Deoxyribose phosphodiesterase excises the residual deoxyribose phosphate unit and DNA poly 1 inserts an undamaged nucleotide. The strand is finally sealed with DNA ligase.

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19
Q

Describe Nucleotide excision repair

A

this fixes everything but doesn’t come into play until necessary, repairs everything, idea is to cut short patches b/w mismatch, cuts the sequence out, once cut up, these proteins are involved in this UvrABCD, the reason why this repair system is used last is because it uses energy

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20
Q

What underlying disease effects the nucleotide excision repair?

A

Xeroderma pigmentosum

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21
Q

Describe Ames test

A

Tests the mutagenicity of different compounds. Is used by FDA to test many chemical rapidly and inexpensively. Uses special bacteria that are very sensitive to many mutagenic agents.
-This test is used to find mutagens. It tests positive if the bacteria grow. This means it will transform the histamine into a normal gene so it can replicate.

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22
Q

What are the 3 pyrimidine bases?

A

cytosine, thymine, and uracil

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23
Q

What are the 2 purine bases?

A

adenine, guanine

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24
Q

Which base structure is smaller?

A

Pyrimidine

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25
Q

Which base structure is larger?

A

Purine

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26
Q

What is the shape, screw sense, and the number of base pairs per turn of helix of DNA-A?

A

Broadest, Right handed, and 11

27
Q

What is the shape, screw sense, and the number of base pairs per turn of helix of DNA-B?

A

Intermediate, right handed, and 10.4

28
Q

What is the shape, screw sense, and the number of base pairs per turn of helix of DNA-Z?

A

Narrowest, Left handed, and 12

29
Q

What is denaturation?

A

the conversion of DS DNA to SS DNA

30
Q

What is denaturation?

A

the conversion of SS DNA to DS DNA

31
Q

What is recombination in DNA?

A

its a repair system that repairs DNA breaks by retrieving sequence information from undamaged DNA which is accomplished by the double-strand break (DSB) repair pathway.

32
Q

What is recombination important for?

A

Generate genetic diversity and generate diversity in antibodies

33
Q

What are the 2 types of recombination?

A

homologous and transposition

34
Q

Does homologous recombination need a homologous sequence? Does it need a RecA protein?

A

Yes and yes

35
Q

Does transposition recombination need a homologous sequence? Does it need a RecA protein?

A

No and no

36
Q

How does homologous recombination work?

A

General recombination requires the breakage of double helices, beginning with a single strand breakage. RecA recognizes the DOUBLE strand break. When a double stranded break occurs, the 3’ OH end finds homo sequences and then uses this to cross over creating the holiday junction. The site of exchange can occur anywhere (wherever there is a cut as long as you have homo sequence). A strand of one DNA molecule has become base-paired to a strand of the second DNA to create heteroduplex joint. No nucleotide sequences are altered

37
Q

What is the protein involved in recombination?

A

RecA is the protein involved which uses energy (ATP) to slide into the breaks and uses this to show DNA polymerase what needs to be fixed. This has multiple binding sites

38
Q

How do Transposons work?

A

Known as the “jumping genes”, Takes one segment and pops it into another place, An enzyme will cut it and insert them into specific sites, make up large portions, This creates diversity, This may be a way that affects what genes gets turned on or off, NO PROTEIN INVOLVED

39
Q

What are 3 the unique problems faced by eukaryotes that are not faced by prokaryotes?

A
  • linear chromosomes with ends
  • much more genetic material
  • much more packaging
40
Q

How many polymerases are in Eukaryotes?

A

5 but we only focus on 3, alpha, delta, and epsilon

41
Q

Describe the function of DNA poly alpha

A

important in primer synthesis and repair, it repairs in the 3’–>5’ exonuclease

42
Q

Describe the function of DNA poly delta

A

polymerase that does leading and lagging strand synthesis as well as repair (like DNA poly 3 in prokaryotes), repairs in the 3’–>5’ exonuclease

43
Q

Describe the function of DNA poly epsilon

A

polymerase that does repair and gap filling on lagging strand, goes in both 3’–>5’ and 5’–>3’ exonuclease (like DNA poly 1 in prokaryotes) removes primer and fills in gaps

44
Q

What are the signals of the origins of replication in the Eukaryotes?

A

Licensing Factors

45
Q

What are the functions of telomeres in eukaryotic replication?

A

Telomeres closes the gaps at the end of replication process, sealing ends with chromosomes which protects the chromosomes and promotes genome stability, the more longer telomeres the greater protection of the telomeres. It also prevents chromosome shortening
(Telomeres are GC rich and have single stranded 3’OH overhangs)

46
Q

What is the function of telomerase in eukaryotic replication?

A

After RNA primers are at the 5’ ends they are removed, leaving a gap, where telomerase fills the extension (RNA specific type of activity), it leaves a 3’OH end sticking out for DNA polymerase to extend using this 3’OH group making ligase available to seal

47
Q

What is the both component of bases and protein structure in DNA (eukaryotes)?

A

Chromatin

48
Q

DNA is packaged into condensed compact structures called what?? HINT: (DNA + histones)

A

Nucleosomes

49
Q

Nucleosomes are a complex of DNA that have several small basic ______ which contain many (+) residues (ARG and LYS). This promotes the interaction of the _____ with the (-) sugar phosphate backbone of DNA

A

Histones

50
Q

What are the 5 classes of histone proteins?

A

H1, H2A, H2B, H3, H4

51
Q

What histones complete the histone octamer AKA the core particle?

A

H2A, H2B, H3, and H4

52
Q

Once you have the histone octamer, then H1 comes in making it a ____?

A

Nucleosome

53
Q

What separates nucleosomes in DNA?

A

Linker DNA

54
Q

What does H1 interact with in DNA?

A

It interacts with the core particle (histone octamer) and the linker DNA

55
Q

Nucleosomes initially organize DNA into coiled structures which forms as a result of cooperative interactions b/w _____ subuntis in between core particle 1 and core particle 2

A

H1

56
Q

RNA & DNA can be hydrolyzed by
specific enzymes called _______
or by certain chemical treatments. What do they do?

A

Nucleases, hydrolyze the

phosphodiester bonds of DNA &/or RNA

57
Q

What do Ribonucleases (RNases) do?

A

Degrade RNA

58
Q

What do Deoxyribonucleases (DNases) do?

A

Degrade DNA

59
Q

______ is the INHIBITOR OF REPLICATION AND TRANSCRIPTION

A

Cisplatin

60
Q

What base pairs have the higher melting temperature?

A

GC has higher melting temp and is more stable

61
Q

If histones were negatively charged, how would this impact eukaryotic DNA?

A 
It wont compact the DNA tightly 
Histones are (+) which help bind to the (-) backbone of DNA helping it condense
62
Q

How do endonucelases work?

A

They cuts in between

63
Q

How do exonucleases work?

A

They chews from either end

Biochemistry I (7 decks)

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