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Molecular > Test One > Flashcards

Test One Flashcards

1
Q

What are the four characteristics of genetic material?

A
  1. Variation through mutation 2. Storage of info 3. Expression of genetic material 4. Replication
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2
Q

Describe the Griffith Experiment.

A

He performed a transformation experiment. He injected mice with a virulent ( IIIS) and avirulent (IIR) strain of bacteria. Determined that the presence of a capsule made the strain virulent, even if the bacteria was dead it could “transform” its DNA into the living bacteria.

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3
Q

Avery MacLeod and McCarty experiment.

A

Determined that DNA is the genetic material by placing heat killed IIIS bacteria cells in a tube with IIR cells along with protease, ribonuclease, and deoxyribonuclease. Transformation occurred within the tubes containing protease, and ribonuclease indicating that they were not the genetic material, and no transformation occurred with the deoxyribonuclease.

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4
Q

Where are glycosidic bonds found?

A

Carbohydrates

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5
Q

What bonds hold together Nucleic Acids?

A

Phosphodiester

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6
Q

Telomeres?

A

Preserves the ends of chromosomes by not allowing the ends to be clipped off during replication. Telomerase is a reverstranscriptase that lengthens telomeres for a given amount of time. As we age the expression of telomerase decreases.

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7
Q

Compare and Contrast the two nucleic acids.

A

DNA:

  • Storage
  • 2X stranded
  • Deoxyribose sugar
  • C,T=Pyrimidines
  • A,G=Purines

RNA:

  • Transportation, catalysis, and regulation of materials
  • Single stranded
  • Ribose sugar
  • C,U= Pyrimidines
  • A,G= Purinea
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8
Q

What bonds hold together Lipids such as triacylglycerol or phospholipids?

A

Ester

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9
Q

Describe the Hershey and Chase experiment.

A

They used radioacticve sulfur and phosphorous to determine which cell type could be mutated to create more bacteria phages.

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10
Q

Where can slighthly compacted chromatin be found at in the cell cycyle?

A

Interphase/G1

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11
Q

What phase do sister chromatids exisit in?

A

S-phase

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12
Q

Compare and Contrast Heterochromatin and Euchromatin.

A

Heterochromatin:

  • Compacted look
  • Repressed activity
  • High histone density
  • CHromosomes located telomeres, centromeres, and repetetive regions
  • Repressed genes
  • Replication is later in S phase

Euchromatin:

  • Uncoiled appearance
  • Active
  • Low histone density
  • Chromosome located in coding DNA regions
  • Actively expressed genes
  • Replication early S phase
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13
Q

Insulator Sequences

A
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14
Q

____ promotes euchromatin through disruption of the histone-DNA interactions.

_____________remodels histones by calling other proteins to the site to incresase or decrease histone density within DNA.

____ activates transcription.

____ Allows expression sometimes

____ Never allows transcription

A

Acetylation

Ubiquitination and Phosphorylation

H3K4me3

H3K27me3

H3K9me3

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15
Q

What amino acids can be acetylated?

A

Lysines

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16
Q

What amino acids can be methylated?

A

Lysines (Lys, K) and Arginines (Arg,R)

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17
Q

What amino acid can be phosphorylated?

A

Serine

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18
Q

What are the writer proteins for Acetyl, Methyl, Phosphate, and Ubiquitin marks?

​

A
  • Acetyltransferase (HAT)
  • Methyl Transferase (HMT)
  • KInase
  • Ubiquitin Ligase (U3)
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19
Q

What are the eraser proteins for Acetyl, Methyl, Phosphate, and Ubiquitin marks?

​

A
  • Deacetylase (HDAC)
  • Demethlylase (HDM)
  • Phosphatase
  • Deubiquitinating Enzyme (DUB)
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20
Q

A heritable change in gene expressions without changing the DNA sequence is known as _____.

A

Epigenetics

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21
Q

T or F Histone marks are not heritable.

A

False- they are heritable

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22
Q

Watson and Crick?

A

First 3D model of a double helix

23
Q

Describe the Meselson and Stahl Experiment.

A

Used Nitrogen 14 and 15 isotopes to follow DNA replication in order to determine if replication was conservative, dispersive or semiconservative.

24
Q

Steps to DNA Replication:

A
  1. Initiation
    • Licensing and Firing
  2. Elongation
    • addition of nucleotides to the 3’ end
  3. Termination
    • Detangle strands remove primers and other proteins
25
Q

Where does the formation of Pre-RC occur and what is the signifigance?

A

Occurs in G1 in the Licensing stage of initiation. The significance of Pre-RC is that it allows for replication bubble to be closer to initiation.

26
Q

What is Pre-RC assembled from?

A

ORC: binds to chromatin assigning that area as an origin of rep.

MCM Complex: forms core of helicase complex, two are loaded at the origin site head to head

27
Q

What makes up the functional helicase complex of Initiation Firing?

A

CMG Helicase composed of: Cdc45, McM2-7 Hexamer, and GINS tetramer

28
Q

What step in DNA replication does this occur?

  • DNA Pol ε is loaded onto the leading strand
  • Melting of the DNA double strands occurs
  • Reconfiguration of the helicase to associate with a single strand (leading one)
A

Part of the firing stage of initiation, activating the helicase complex

29
Q

Describe Elongation.

A

Nucleotides are added to the 3’ end of DNA allowing for growth in a 5’ to 3’ direction.

30
Q

What are the four major steps to synthesize a new strand of DNA in elongation.

A
  1. Add RNA primers ( primase)
  2. Add dNTPs (DNA Polymerase α)
  3. Remove RNA Primers (RNaseH)
  4. Seal nicks in the backbone (DNA Ligase)
31
Q

What are RPC and PCNA?

A

RPC is the clamp loader found in eukaryotic organisms and it adds PCNA the sliding clamp. PCNA is also a processivity factor in DNA elongation

32
Q

What are the differences between Prokaryotic and Eukaryotic Elongation?

A

Prokaryotes:

  • 1000nt/sec
  • Primase partner=helicase
  • Name of sliding clamp is that
  • Name of clamp loader is that
  • Elongating pol. is DNA Pol III
  • ssDNA Binding is that
  • RNA primers are replaced by DNA Pol I

Eukaryotes:

  • 50 to 100 nt/sec
  • Primase partner is Polymerase α
  • Sliding clamps is PCNA
  • Clamp loader is RPC
  • Elongating pol. is DNA Pol Ɛ (lead) and DNA Pol δ (lag)
  • ssDNA binding is Replication Protein A
  • DNA Pol δ replaces RNA Primers
33
Q

How are RNA primers removed in elongation?

A

DNA Pol δ moves the RNA primer out of place in order to continue with synthesizing DNA until the next okazaki fragment. Then FEN1 clips off the RNA tail and DNA Ligase seals the nick.

34
Q

Topoisomerase I and II.

A

come back to.

35
Q

Describe Termination.

A

RNA primers are removed by DNA pol δ, and the MCM complex is ubiquinated which signals for degradation. Topoisomerase II removes helix tangles due to the superhelical stress as replication forks get closer.

36
Q

T or F histones can be recycled?

A

True- histones are recycled in order to propagate messages along on the new daughter strands.

37
Q

What is FACT?

A

Histone remodeling

FACT knocks off histones in front of the replication fork.

After the new strand has been replicated AFC1 replaces the histones by binding H3-H4 diners and delivering them to CAF1.

38
Q

T or F DNA Replication is the only time histone remodelilng can occur?

A

False-

39
Q

What polymerases have an exonuclease domain, and which is the best?

A

alpha delta and epsilon, which means they can proofread.

Delta is the best proofreader and alpha is the worst.

40
Q

What are the steps to proofreading?

A
  1. Sense the incorrect shape
  2. Stall the replication fork
  3. Move the wrong nucleotide to the exonuclease domain
  4. Cleave the phosphodiester bond
  5. Move the stand back into the polymerase domain and begin
41
Q

Match the Polymerase with the correct Repair Mechanism.

(Polß, Rev1, TdT, Pol µ, Pol λ, Pol δ, Pol K, Pol ε, Pol η, Pol I,PolZ)

Repair Mechanism

Repair Polymerases

Base Excision Repair

Non-Homologous End Joining

Translesion Synthesis

Nucleotide Excision Repair

A

Repair Mechanism

Repair Polymerases

Base Excision Repair

Pol ß and Pol λ

Non-Homologous End Joining

TdT and Pol ε, Pol µ

Translesion Synthesis

Rev1 and Pol Z, Pol I, Pol n

Nucleotide Excision Repair

Pol ε Pol K, and Pol δ

42
Q

What types of mutations does base excision repair fix?

A

Tautomers and modified nitrogenous base erros due to mutations in hydrogen bond potentials.

43
Q

What kind of repair fixes mutation from error prone repair due to raod blocks such as depurination and covalent adducts?

A

Translesion synthesis and Nucleotide excision repair

44
Q

What does a Glycosylase do?

A

Part of Base Excision Repair:

Recognizes modified nucleotides, it can “scan” to find errors.

Each modification has its own specific glycosylase that recognizes it.

The base is swung out and clipped off at the glycosidid bond.

45
Q

What is an AP Endonuclease?

A

Part of Base Excision Repair:

Cleaves a phosphodiester bond on both sides of the apurinic (abasic) site

creating a single strand break.

46
Q

How does BER work?

A

Glycosylases clip off the base, an AP Endonuclease creates a single stranded break, and Pol Beta or Lambda adds the correct nucleotide, followed by DNA Ligase to repair the phossphodiester bond.

HIGH repair accuracy

47
Q

How does NER work?

A

UV Repair Enzymes recognize something is off within the helix and cleave the surrounding 10-30 nt on that particular strand.

TF II is the helicase that will unwind the region that is going to be clipped

Pol Epilson (If Replication is actively occurring) or Pol Delta/Kappa (Quiescent cells-not actively replicating) add back the nucleotides

DNA Ligase repairs the phosphodiester bond

HIGH repair accuracy

48
Q

How does Translesion Synthesis work?

A

Translesion Polymerases take over DNA synthesis, through covalent modifications to PCNA, to push past the error. They don’t repair- just get passed the lesion.

LOW accuracy

49
Q

What are inserters in TLS?

A
  • Rev1:
  • Pol n:
  • Pol I:
50
Q

What are the extenders in TLS?

A

Pol Z and Pol n

51
Q

Nonhomologous End Joining?

A

Ends are prepared for ligation by Ku70/Ku80 (Kinases) and Artemis nuclease cuts into the helix and DNA is removed at the ssDNA site.

TdT, Pol mu, and Pol Lambda bridge the gap created by the Artemis nuclease. Tdt can persorm the untemplated synthesis.

DNA Ligase IV adds the phosphodiester bond.

LOW accuracy for repair.

52
Q
A
53
Q
A

Molecular (10 decks)

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