1. Molecular Biochemistry Flashcards
1
Q
Which histone ties DNA-histone nucleosome beads into more condensed structures?
A
H1. The only histone that is not in the nucleosome core.
2
Q
DNA loops twice around histone octamer to form nucleosome bead. Which histones are these?
A
Histones H2A, H2B, H3, H4
3
Q
Is DNA acidic or basic?
A
acidic
4
Q
What type of aa are histones made of? Are they acidic or basic?
A
lysine and arginine; basic
5
Q
Which is more accessible to transcription factors: heterochromatin or euchromatin?
A
Euchromatin
6
Q
If a cell has a hyperchromatic nucleus, will it undergo transcription?
A
No. Heterochromatin are condensed, transcriptionally inactive and sterically inaccessible.
7
Q
What are chromosomes? During what part of the cell cycle are they found? In what pathologic state would you see a lot of chromosomes?
A
Highly condensed forms of DNA; mitosis;
Neoplasia- highly dividing and thus hyperchromatic
8
Q
What experiments look at chromosomes?
A
karyotyping
9
Q
Heterochromatin and euchromatin: which have more methylated and/or acetylated histones?
A
Hypermethylation inactivates transcription (heterochromatin). Histone acetylation relaxes DNA coiling, allowing for transciprtion (euchromatin)
10
Q
What does guanine have on it?
A
a ketone
11
Q
What does thymine have on it?
A
a methyl
12
Q
Deamination of what pyrimidine makes what?
A
cytosine to uracil
13
Q
In what genetic code is uracil found in?
A
RNA
14
Q
How many hydrogen bonds does a G-C and A-T connection have? Which one has a higher melting temperature?
A
GC (3) and AT (2). GC has a higher melting temperature because of the additional hydrogen bond.
15
Q
What amino acids are required in purine synthesis and/or pyrimidine synthesis?
A
G-A-G (glycine, aspartate, glutamine) and Formyl-tetrahydrofolate for purine synthesis. Aspartate for pyrimidine synthesis.
16
Q
What is the difference between a nucleotide and a nucleoside?
A
NucleoSide=base+ribose (Sugar)
NucleoTide=base+ribose+phosphaTe
17
Q
Is PRPP added later or first in pyrimidine synthesis?
A
Later. Make temporary (orotic acid) base first, then ad surgar+phosphate (PRPP) and modify base.
18
Q
What is PRPP? How is it made?
A
It is the ribose+phosphate; its made from PRPP synthetase + ATP using Ribose 5-P from the HMP shunt
19
Q
What is the precursor for both purines?
A
IMP
20
Q
What is the precursor for pyrimidines?
A
Orotic acid (plus PRPP) to make UMP -> UDP
21
Q
Which intermediate is involved in both pyrimidine synthesis and the urea cycle?
A
Carbamoyl phosphate (which becomes orotic acid)
22
Q
Why does a deficiency in ornithine transcarbamoylase result in an increased production pyrimidine?
A
Ornithine transcarbomoylase deficiency leads to an accumulation of carbamoyl phosphate, converting to orotic acid, the precursor of pyrimidine.
23
Q
Is Carbamoyl phosphate synthetase I or II involved in pyrimidine synthesis?
A
CPS I (mitochondria, urea cycle) CPS II (cytosol, pyrimidine metabolism)
24
Q
What three enzymes lead to orotic acid accumulation? what reactions are they involved in?
A
Ornithine transcarbamoylase (urea cycle, accumulation of carbamoyl phosphate) Orotic acid phosphoribosyltransferase and Orotidine 5'-phosphate decarboxylase (conversion of orotic acid to UMP)
25
What step in pyrimidine synthesis requires aspartate?
Conversion of carbamoyl phosphate to orotic acid (orotic acid phosphoribosyltransferase, orotidine 5'-phosphate decarboxylase)
26
What are the clinical symptoms of orotic aciduria?
Increased orotic acid in urine, megaloblastic anemia (does not improve with admin of vit B12 or folic acid), failure to thrive. No hyperammonemia (vs. OTC deficiency - increase oritic acid with hyperammonemia)
27
How do you differentiate the causes of orotic aciduria?
No hyperammonemia=defect in orotic acid hosphoribosyltransferase or orotidine 5'-phosphate decarboxylase (autosomal recessive)
Hyperammonemia=ornithine transcarbamoylase deficiency
28
What is unique about megaloblastic anemia from increased orotic acid?
Orotic aciduria megaloblastic anemia can not be corrected with folic acid or vit B12
29
How do you treat orotic aciduria? What is the mechanism for treatment?
oral uridine administration; provides nucleosides and provides feedback inhibition
30
What converts dUMP to dTMP? What drug blocks this?
Thymidylate synthase; 5-Fluorouracil
31
What enzyme is involved in convert UDP to dUDP? What drug blocks this?
Ribonucleotide reductase; hydroxyurea
32
What does ornithine transcarbamyolase do to carbamoyl phosphate?
Converts carbamoyl phosphate to citrulline
33
What does 6 mercaptopurine do?
6MP blocks de novo purine synthesis
34
Other than thymidylate synthase, what else is required to convert dUMP to dTMP?
N5N10 methylene THF
35
After N5N10 methylene THF donates a methyl for conversion of dUMP to dTMP what is it converted to?
DHF
36
What enzyme converts DHF to THF? What vitamin cofactor is used to transfer a methyl from an amino acid to DHF? What amino acid is that?
Dihydrofolate reductase; vitamin B12; homocysteine
37
What happens to homocysteine after converting a methyl?
Homocysteine becomes methionine
38
how is THF converted to N5N10 Methylene?
Using serine (which turns into glycine after reaction)
39
what does methotrexate do? what step is this enzyme involved in?
it inhibits conversion of DHF to THF by blocking dihyrdofolate reductase
40
what is the difference between methotrexate and trimethroprim?
trimethroprim inhibits bacterial dihyrofolate reductase
41
what is adenosine/AMP converted to? through what enzyme?
inosine/IMP; adenosine deaminase
42
GMP is degraded to guanosine which is degraded to guanine. What two options are next? by what enzymes?
either salvage by HGPRT and PRPP or converstion to xanthine and then to uric acid by xanthine oxidase
43
IMP is degraded to inosine and then to hypoxanthine. what two options are next? by what enzymes?
either salvage by HGPRT and PRPP or conversion to xanthine and then uric acid by xanthine oxidase
44
in what syndrome is HGPRT deficient? what is the inheritance pattern?
Lesch Nyhan syndrome; X linked recessive
45
what is main lab finding in Lesch Nyhan syndrome? due to what enzyme deficiency? what reaction is deficient?
uric acidemia; HGPRT; purine salvage
46
what are the main clinical symptoms of Lesch Nyhan syndrome?
self mutilation, aggression, mental retardation, gout, hyperuricemia, choreathetosis
47
what is the major cause of SCID? what does SCID stand for?
adenosine deaminase deficiency; Severe combined immunodeficiency disease
48
what is the link between adenosine deaminase deficiency and decreased lymphocyte count?
excess ATP and dATP has negative feedback inhibition on ribonucleotide reductase which results in decreased DNA synthesis and thus decreased lymphocyte count
49
what has negative feedback inhibition on ribonucleoside reductase?
ATP and dATP
50
what is methotrexate?
a folic acid analogue
51
what is given to prevent side effects when methotrexate is given? why does this work?
folinic acid; does not require DHF
52
in the genetic code, what does unambiguous mean?
each codon specifies only one amino acid
53
what does degenerate/redundant mean in terms of the genetic code?
codons may encode same amino acid since there are only ~20 aa
54
what structures allows for degeneracy?
tRNA wobble
55
what is the exception to degeneracy in the genetic code?
methionine is only encoded by AUG
56
what is the exception to the nonoverlapping/commaless aspect of the genetic code?
some viruses
57
what is the exception to the universal aspect of the genetic code?
mitochondria, archaebacteria, mycoplasma, and some yeasts
58
what are the three types of point mutations?
silent, misssense, nonsense
59
what is a clinical example of a missense mutation?
sickle cell disease- conversion of hydroophillic glutamic acid to hyrdophobic valine
60
what is an example of a nonsense mutation?
beta thalassemia
61
what creates a frameshift mutation? what are some clinical examples?
insertion or deletion of a number of nucleotides indivisible by 3; tay sachs, duchennes MD
62
what does topoisomerase do? I or II eukaryotic?
creates nicks in DNA to prevent supercoiling; both!
63
what is DNA gyrase?
a topoisomerase II
64
what Ab class blocks DNA gyrase?
Flouroquinolones
65
what is bleomycin?
an anti cancer agent that is a topoisomerase II and creates nicks in DNA
66
what is etoposide? why does this not affect normal healthy cells?
a topoisomerase II inhibitor; because cancer cells use II more so than healthy cells
67
what type of polymerase is primase?
DNA dependent RNA polymerase
68
what type exonuclease activity does DNA polymerase III have? in what organisms is it found?
3'--\> 5'; prokaryote only
69
what type of exonuclease activity does DNA polymerase I have? in what organisms is it found? what is it used for?
5'--\> 3'; prokaryote only; for removing RNA primer and filling it with DNA
70
what type of drug are alkylating agents? how do they work? give a couple examples
antineoplastic agents; alkylate DNA!; cyclophosphamide and nitrosurea (aka lomustrine- a nitrosource)
71
what two anti-neoplastic drugs work by blocking DNA and RNA polymerase?
dactinomycin, doxorubicin
72
name two antineoplastic drugs that work by inhibiting the mitotic spindle by MT blocking.
vincrstine (vinca alkaloids) and paclitaxel
73
how are senescent cells different from some neoplastic and germ cells? what does this substance do?
telomerase; an RNA polymerase that uses a RNA template to add DNA to the end of shortening 3' ends
74
what four enzymes are required for nucleotide excision repair?
endonucleases, exonucleases, DNA polymerase, DNA ligase
75
what is the difference between exonucleases and endonucleases?
endonucleases are specific and break specific linking phosphodiester bonds, exonucleases are not sequence specific and just remove the nucleoside
76
what type of enyzmes are used in base excision repair?
glycosylases (only remove the base- cut the bond between ribose and base)
77
what is needed after the glycosylase in base excision repair?
an AP (apyrimidinic) endonuclease to cut the DNA, exonuclease then removes and then filled and sealed by enzymes
78
what is most often mutated in xeroderma pigmentosum? what is the inheritance pattern? what are the clinical symptoms?
UV specific endonucleases for excision repair; AR; dry skin, photosensitivity, poikiloderma, susceptibility to skin cancers
79
to what type of DNA damage are xeroderma pigmentation susceptible to?
UV nonionizing radiation causing thymidine dimers
80
how does mismatch repair work? in what cancer is it mutated? what type of DNA is methylated?
immediately after replication, DNA is unmethylated and so it is a signal to be double checked; HNPCC; heterochromatin
81
what kind of DNA damage does ionizing radiation cause? what type of repair helps with this?
double strand breaks; nonhomologous end joining
82
which end carries the triphosphate? which end of DNA makes the hydoxyl attack?
5' end; 3' end
83
what aa does AUG mRNA code for in eukaryotes? prokaryotes?
methionine; f Met (formyl methyl methionine)
84
what is the difference between the promoter and enhancer? in what process are they used for?
promoter binds RNA Pol II and is very close (25 bases) to initiation site and is AT rich; enhancer/silencers bind TFs only, can be located close or far and regulate gene expression but not specifically initiation; transcription
85
what do enhancers/silencers bind?
TFs
86
do RNA polymerases have proofreading function? what does this mean for HIV?
no; increased mutation rate!
87
which RNA polymerase synthesizes tRNAs and snRPs?
III
88
which RNA polymerase synthesizes rRNA? where?
I; nucleolus
89
how many RNA polymerases do prokaryotes have? what drug blocks prokaryotic RNA polymerase only? what is it used for?
1 for all three classes of RNA; Rifampin; TB
90
What toxin causes liver failure by inhibiting RNA polymerase II if ingested? where does it come from?
alpha amanitin; mushroom caps
91
what three steps are included in RNA processing? where does it occur?
5' capping (with 7 methylguanosine), 3' adenylation, splicing of introns; nucleus
92
what is the signal for adenylation? what enzyme does? does it require a template?
AAUAAA; Poly A polymerase; no
93
what is the RNA called before processing? and after?
hnRNA; mRNA
94
what are required for splicing? encoded by what polymerase?
snRNPs; RNA polymerase III
95
in what disease are there antibodies to snRNPs?
Lupus
96
do introns or exons contain the genetic information?
exons
97
what is alternative splicing? in what disease state does alt splicing occur unintentionally d/t early stop codons?
when different combination of exons get combined together; in Beta thallasemia
98
where does splicing occur?
nucleus
99
what are heat shock proteins?
assist in spontaneous refolding of proteins
100
like mRNA has a poly A tail on the 3' end, what does tRNA have on its 3' end? what happens here?
CCA and chemically modified bases where amino acid is covalently bonded
101
what is "charging" of tRNA? what enzyme regulates this? what does this reaction require? in what process is this?
when the amino acid is covalently binded to its corresponding tRNA; Aminoacyl tRNA synthetase; ATP; translation
102
at what point is the amino acid correspondence to the mRNA code finalized?
in the charging reaction! for this reason aminoacyl tRNA synthetase double checks
103
after addition of an aa, where does the aminoacyl tRNA now bind to?
30S ribosomal RNA (small one)
104
what Abs block the binding between aminoacyl tRNA and rRNA by binding the 30S ribosome?
aminoglycosides and tetracyclines
105
what toxins prevent elongation in translation in humans (by binding 40s)?
shiga toxin and ricin (protein in castor beans)
106
what is significant about 50S/60S ribosomal unit?
it contains the peptidyltransferase activity (for elongation of protein
107
what antibiotic inhibits peptidyltransferase activity?
chloramphenicol
108
what fungicide/rat repellent inhibits the peptidyltransferase activity in humans?
cycloheximide
109
Initiation of protein tranlsation is activated by ATP hydrolysis. T/F?
False; GTP hydrolysis
110
Prokaryotes have what ribosomal units?
30S + 50S= 70S
111
In protein translation, what is the "A" site for? "P" site? "E" site? what is the exception to this?
Incoming Aminoacyl tRNA; site where peptidyltransferase bond is made between growing peptide aa's; the holds the empty tRNA as it exits; the initiator mRNA (met or f-met) starts off in E site rather than A site
