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COMLEX Prep > All in one > Flashcards

All in one Flashcards

1
Q

What is the condensed structure of DNA?

A

DNA is formed into chromatin as it wraps around positively charged protein called histone proteins. It typically wraps around twice, and then H1 and a linker protein binds to commplete the structure. DNA has a negative 2 charge because of the phosphate backbone, so it can easily bind to the histone protein.

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2
Q

How it mitochondrial DNA different from nuclear DNA?

A

Mitochondrial DNA is circular and is not wrapped around histone proteins.

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3
Q

What are the positively charged proteins in histone proteins?

A

Lysine and arginine. Think LARge DNA needs condensed. L - Lysine Ar - Arginine

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4
Q

Heterochromatin vs. Euchromatin

A

Heterochromatin is very condensed DNA and shows up darker on EM. It is transcriptionally inactive. There is more DNA methylation and less histone acetylation.

Euchromatin is loosely packed DNA, it is transcriptionally active and shows up lighter on EM images. DNA is less methylated and histones are more acetylated.

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5
Q

What is DNA methylation?

A

Makes DNA less likely to be transcribed. Typically methylated at CpG islands, specifically within gene promoter regions.

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6
Q

How are Barr bodies created? What condition is often associated with dysregulated DNA methylation of the X chromosome?

A

Intense methylation of the X chromosome. THe condition is Fragile X Syndrome.

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7
Q

What is histone methylation?

A

Histone methylation typically causes reversible transcriptional suppression, but it is possible for activation. Methylated at lysine and arginine.

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8
Q

What is histone acetylation?

A

Histone acetylation is when acetyl groups are added to histone proteins to remove the positive charge on the protein so DNA is less tightly packed. An example of this is the thyroid hormone receptor, when it is acetylated thyroid hormone synthesis is altered.

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9
Q

What is histone deacetylation often involved in?

A

Could be an explanation for Huntington’s Disease. Deactivates DNA transcription.

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10
Q

nucleoside vs nucleotide

A

A nucleoside is a sugar and a nitrogenous base. A nucleotide is that with a phosphate bond

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11
Q

Purines and pyrimidines

A

Purines are as pure As Gold, they contain 2 rings.
Pyrimidines only have one ring, they are CUT. CUT the py

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12
Q

How are purine hydrogen bonds different from pyrimidine hydrogen bonds?

A

Purine hydrogen bonds exist in 3’s, meaning they are stronger and require a higher melting temperature to denature. Pyrimidines only have 2.

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13
Q

What are the deamination reactions for cytosine, guanine, adenine, and 5-methylcytosine?

A

Cytosine –> uracil
adenine –> hypoxanthine
guanine –> xanthine
5-methylcytosine –> thymine

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14
Q

How are uracil and thymine different?

A

Methylate uracil to make thymine

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15
Q

Structures of the nitrogenous bases.

A

This image

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16
Q

In what direction does DNA replication occur and how is it different in prokaryotes and eukaryotes?

A

In the 5’ to 3’ direction. In eukaryotes, it is more complex, but in both it is semi conservative, meaning in each cycle one strand from parent is reused while the other is replicated.

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17
Q

Origin of replication differences in prokaryotes and eukaryotes?

A

in prokaryotes there is one site and in eukaryotes there are multiple. Often contain AT rich regions, like TATA boxes.

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18
Q

What protein is deficient in Bloom Syndrome?

A

Helicase mutation in BLM gene

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19
Q

What are single stranded binding proteins?

A

Protein that bind to separated DNA strands during replication to prevent degradation and to prevent reannealing.

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20
Q

What are the different types of DNA topoisomerses?

A

In eukaryotes there is type I and type II, type 1 creates a single stranded break and can relieve negative (and sometimes positive in eukaryotes) supercoils and type II can relieve positive supercoils through double stranded breaks. In E.coli, tp II is DNA gyrase.

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21
Q

Which protein helps form primer for DNa replication

A

Primase

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22
Q

Types of DNA polymerase in prokaryotes

A

III - elongation of leading and lagging strand. 5’ to 3’ synthesis, 3’ to 5’ exonuclease ability
I - Degrades RNA primer and replaces with DNA, 5’ to 3’ exonuclease ability

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23
Q

What is telomerase

A

It is a reverse transcriptase that can add DNA to the end of a DNA strand to prevent loss of genetic information. Upregulated in progenitor cells and cancer cells, in aging and progeria.

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24
Q

What is non homologous end joining

A

A double stranded break can be repaired by joining two strand of DNA together, strands do not have to be homologous. Translocation possible. Dysfunctional in ataxia telangiectasia.

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25
Q

Homologous recombination

A

When a double stranded break occurs and instead of joining the ends, a template strand is used to replicate the missing fragments. Intact DNA is split and broken fragments split, each using one of intact strands to reconstruct the DNA. defective in breast and ovarian cancers with BRCA1/2 mutations. And in Franconia anemia.

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26
Q

Nucleotide excision repair

A

When specific nucleotides, such as pyrimidine dimers, are repaired through a mechanisms where endonucleases remove the damaged bases and DNA polymerase/ligament fill and seal. Occurs in G1. Defective in xeroderma pigmentosa

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27
Q

Presentation of xeroderma pigmentosa

A

Dry skin, photosensitivity, and skin cancer. NER deficiency

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28
Q

What is base excision repair?

A

Base specific glycosylase removes single nucleotide (say deamination of C to U) and leaves apurinic/apyrimidic site

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29
Q

Mismatch repair

A

Longer strand containing mismatched DNA (unmethylated site) gap is filled and sealed occurs in S phase.

30
Q

What process is defective in Lynch Syndrome, or hereditary nonpolyposis colorectal cancer?

A

Mismatch repair

31
Q

Pyrimidine and purine synthesis pathways

A

this image

32
Q

Which drug blocks the production of orotic acid in pyrimidine synthesis pathway?

A

leflunomide inhibits dihydrooritate dehydrogenase

33
Q

What part of pyrimidine synthesis does 5-fluorouracil/capecitabine inhibit?

A

thymidylate synthase, forms 5-F-dUMP which prevents formation of dTMP

34
Q

What part of purine synthesis pathway does 6-mercaptopurine (6-MP)/
azathioprine

A

It inhibits the de novo synthesis pathway for purines, specifically the conversion of PRPP to IMP through guanine phosphoribosyltransferase

35
Q

What do Mycophenolate and ribavirin inhibit in the purine synthesis pathway?

A

THey inhibit the conversion of IMP to GMP through inosine monophosphate dehydrogenase

36
Q

How does hydroxyurea affect the purine/pyrimidine synthesis pathway?

A

It inhibits ribonucleotide reductase, therefore preventing conversion of ribonucleotides to deoxyribonucleotides.

37
Q

What role does Methotrexate (MTX), trimethoprim (TMP),
and pyrimethamine play in the purine/pyrimidine synthesis pathway

A

They all block different species’ dihydrofolate reductase. Methtrexate (huMans), Trimethoprim (bacTeria), and Pyrimethamine (Protozoa). Essentially, less THF production from DHF and less dTMP

38
Q

What is the role of carbamoyl phosphate synthetase II? How to remember the difference between that and CPSI?

A

CPSII is in the cyTWOsol, meaning its role is to help with pyrimidine synthesis. CPSI is in the mItochondria, helping out with the urea cycle.

39
Q

What are the different types of mutations in DNA?

A

-Silent is when a nucleotide is changed but the same amino acid results, often in wobble site.
-Missense is when the amino acid is changed as a result of a change, conservative if similar amino acid.
-Nonsense is that in which results in an early STOP codon
-Frameshift mutation is that in which an insertion or deletion occurs and the entire frame of the DNA is shifted whihc results in an entirely new, often non-functional protein.
-Splice site mutation is that in which the mRNA has a retained intron as a result of a mutation in the DNA, which can result in a different protein product.

40
Q

Difference between a transition mutation and a transversion mutation

A

Transition - purine to purine or pyrimidine to pyrimidine
Transversion - Switch between the two types

41
Q

What kind of mutation is often associated with sickle cell disease

A

Missense mutation, glutamic acid to valine

42
Q

What kind of mutation is associated with Duchenne Muscular Dystrophy, Tay Sacchs Disease and CF?

A

Frameshift

43
Q

What kind of mutation is associated with Gaucher Disease, Marfan Syndrome, and some types of Beta-thalassemia

A

Splice site mutations

44
Q

Explain the lac operon and its regulation

A

The lac operon as we know exists in E.coli. The body will always prefer glucose over lactose, but in severe circumstances when glucose is not present the operon is not repressed and lactose can be metabolized.

There are 3 lac genes in the oepron (controlled by same promoter) which are lac Z, Y, and A. Z makes beta-galactosidase (breaks lactose into glucose and galactose), Y makes lactose permease (allows lactose into cell, some toxic ones), and A makes theogalactoside transacetylase (destroyd toxic ones). There is also lacI, not apart of the same operon, that produces lac repressor that binds to the operator to suppress transcription. Also, there is a CAP site which binds CAP which is activated by cAMP.

If no lactose present, only basal rate tranascription of lac genes. Operator is bound by repressor, and if glucose is present then no cAMP to activate CAP.

If lactose and glucose present, then allolactose (inducer) can bind to repressor and prevent its binding to the operator. However, low cAMP so no activation of CAP.

If lactose present and glucose not, then high cAMP activates CAP and it can bind to CAP site to promote transcription, and allolactose bind repressor so lactose genes are being transcribed fully.

If neither present, then CAP may be activated but without lactose, operator still bound.

Adenylate cyclase is blocked by glucose

45
Q

What nitrogenous base is this?

A

Adenine
“Only Amine”, its a purine so two rings

46
Q

What nitrogenous base is this?

A

Guanuine
gO amine

47
Q

Which nitrogenous base is this?

A

Cytosine - The structure left

48
Q

Which nitrogenous base is this?

A

Thymine - T has 3 branches, other pyrimidines do not

49
Q

Which nitrogenous base is this?

A

Uracil - U shape, two identical carbonyls

50
Q

What is the promoter region of DNA?

A

It is where RNA polymerase and other transcription factors bind to begin transcription. Upstream, and contain TATA boxes (proks) and CAAT boxes (euks), AT rich regions. Mutation here typically results in drastically reduced expression.

51
Q

What is an enhancer region?

A

Where activators bind to enhance and upregulate transcription of that gene.

52
Q

What is a silencer region?

A

Where silencers bind to reduce the amount of transcription of that gene.

53
Q

What are epigenetics?

A

Specific alterations to the DNA strand that change the transcription frequency without actually changing the DNA, i.e. methylation.

54
Q

What is the initial pre-mRNA sequence called, and what modifications are made to it?

A

hnRNA. First, while transcription is finishing up, a 7-methylguanosine cap is added to the 5’ end of the hnRNA to protect from degradation and to give stability. THen, Polyadenylation (poly-A polymerase does not need template) of the 3’ end where 200-250 A’s are added to 5’ end to provide stability and protect from degradation. THen, splicing of introns.

55
Q

What are cytoplasmic processing bodies?

A

These are quality control centers for mature mRNA that exit the nucleus and enter the cytosol. Caps are removed, exonucleases are present. mRNA can be destroyed or stores for later.

56
Q

What would a mutation in the Poly A polymerase result in?

A

mRNA that is degraded too early

57
Q

What is the Kozak Sequence?

A

It is the initiation site on the mRNA where the small ribosomal subunit binds. Impairment here means no translation, less protein.

58
Q

What are the 3 types of eukaryotic RNA polymerases?

A

RNA Poly I - Transcribes rRNA in the nucleolus
RNA Poly II - Transcribes mRNA, snRNA, and microRNA. Opens DNA at ori.
RNA Poly III - Transcribes 5S rRNA and tRNA.

They are ordered in the order of their use in translation. First, ribosome travels to mRNA then tRNA is used.

59
Q

What is alpha-amanitin, or the death cap mushroom?

A

Amanita phalloides. It inhibits RNA Polymerase II, causes dysentery (vomitting, diarrhea, intestinal infection) and hepatotoxicity.

60
Q

How many RNA polymerases are present in prokaryotes?

A

Just one, RNA polymerase, it makes all three kinds of RNA.

61
Q

What is dactinomycin?

A

Inhibits all kinds of RNA polymerases from eukaryotes to prokaryotes

62
Q

What do rifamycins do (rifampin, rifabutin)?

A

They inhibit DNA dependent RNA polymerases in prokaryotes, effective antibiotic.

63
Q

What is the advantage of alternative splicing?

A

Alternative splicing is important for forming more than one kind of protein from the same gene by splicing different exons together.

64
Q

The process of splicing pre-mRNA occurs via what mechanism?

A

There are a couple different ways. The frist two ways involve no proteins, just a free G or an internal A within the intron sequence. However, the main mechanism involves a splicesome.

A splicesome, or snRNP, is an snRNA combined with proteins. U1 snRNP binds to the GU at the 5’ end of the intron, and U2 snRNP binds at branch point where there is an A. the 5’ splice site is cleaved, and a lariat loop is made of the intron as the free 5’ end (G) can bind to branch point. Then, the free 3’ OH end can attack the 3’ splice site and fully remove the intron.

65
Q

What conditions are often associated with pre-mRNA splicing issues?

A

Spinal muscular atrophy - snRNP assembly not working because of SMN protein mutation. Results in congenital degradation of anteiror horns, hypotonia or floppy baby syndrome.

SLE - can be associated with anti U1 snRNP antibodies

66
Q

What is the structure of tRNA?

A

It has a CCA sequence leading up to the 3’ end which is where the amino acid will bind (Can Carry Amino). It has a T-arm which helps connect the tRNA to the ribosome. It has a D-arm with dihydrouridine residues which is important in connecting the tRNA to the correct aminoacyl synthetase. And then it has the anti-codon loop, which contains the sequence to which the mRNA will bind for amino acid pairing. It has secondary structure, cloverleaf structure.

67
Q

How is tRNA charged?

A

It is charged by adding an ATP and using aminoacyl-tRNA synthetase. First, ATP and an amino acid react to form amino acid AMP and two pyrophosphates. The amino acid is now charged. Then, through the respective amino acid synthetase, the adenine at the 3’ end of the tRNA can attack the aminoacyl AMP and take the amino acid.

68
Q

What are some of the issues that can occur with tRNA charging?

A

If the wrong amino acid is placed on the tRNA, then it is mischarged and this can lead to mutation. Typically, however, the incorrect amino acid has its bind hydrolyzed.

69
Q

Start codons in prokaryotes and eukaryotes

A

Both are AUG, but in eukaryotes this codes for methionine and in proks it codes for N-formylmethionine.

70
Q

What are the stop codons?

A

UGA
GAA
UAG

U Go Away
U Are Away
U Are Gone

COMLEX Prep (1 decks)

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