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FA: Biochemistry > molecular > Flashcards

molecular Flashcards

1
Q

How is DNA found in the nucleus?

A

DNA is in condensed, chromatin form

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2
Q

How does chromatin condense to get into the nucleus?

A

(-) charge DNA loops 2x around (+) charged histone to form nucleosome bead

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3
Q

What are the common amino acids of histone and what holds the beads on a string together?

A

lysine and arginine where H1 ties nucleosome beads together in a string

Beads (nucleosome core and H1) on a string (DNA)

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4
Q

How is DNA in mitosis?

A

DNA condenses to form chromosomes

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5
Q

What are the histones of the nucleosome core? are there any other histones present outside of the core?

A

(2x)nucleosome core histones=> H2A, H2B, H3, H4

H1 only histone not in nucleosome core

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6
Q

describe heterochromatin

A

condensed, transcriptionally inactive, sterically inaccessible

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7
Q

describe euchromatin

A

less condensed, transcriptionally active, sterically accessible

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8
Q

What is the importance of DNA methylation?

A

template strand cytosine & adenine are methylated in DNA replication allowing mismatch repair enzymes to distinguish bw old & new strands in prokaryotes

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9
Q

Result of histone methylation?

A

inactivates transcription of DNA

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10
Q

result of histone acetylation

A

relaxes DNA coiling, allowing for transcription

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11
Q

What are the purines and associated nucleotides?

A

Adenine and guanine => 2 rings

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12
Q

what are pyrimidine and associated nucleotides?

A

cytosine, thymine and uracil => 1 ring

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13
Q

How is uracil made? where is it found?

A

deamination of cytosine gives uracil that is found in RNA

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14
Q

What nucleotide has a ketone? a methyl?

A

ketone=> guanine

methyl=> thymine

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15
Q

What is the binding of the nucleotides? which bond is stronger? what is the significance of more G-C bonding?

A

G-C bond (3H bonds) is stronger than A-T bond (2H bonds)

G-C bonding will increase melting temperature

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16
Q

What are the amino acids necessary for purine synthesis?

A

Glycine
Aspartate
Glutamine

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17
Q

What is needed to make a nucleoside?

A

base + ribose (sugar)

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18
Q

What is needed to make a nucleotide?

A

base + ribose + phosphate;

linked by 3’-5’ phosphodiester bond

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19
Q

What is the difference in purine vs pyrimidine synthesis?

A

purines=> 1) start w/ sugar + phosphate (PRPP)
2) add base

pyrimidines=> 1) make Orotic acid (temp. base)

2) add sugar + phosphate (PRPP)
3) modify base

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20
Q

How are deoxyribonucleotides made?

A

1) ribonucleotides synthesized

2) ribonucleotide reductase converts to deoxyribonucleotides

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21
Q

What are the 2 metabolic pathways that carbamoyl phosphate is involved in?

A

de nono pyrimidine synthesis;

urea cycle

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22
Q

How does ornithine transcarbamoylase deficiency affect pyrimidine synthesis?

A

used in urea cycle that deficiency will accumulate carbamoyl phosphate which is then converted to orotic acid

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23
Q

What amino acid does pyrimidine base production require?

A

aspartate

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24
Q

Where does hydroxyurea mechanism of action work?

A

inhibits ribonucleotide reductase

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25
Q

where does 6-mercaptopurine (6-MP) MOA work?

A

blocks de novo purine synthesis

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26
Q

where does 5-fluorouracil (5-FU) MOA work?

A

inhibits thymidylate synthase (decreases deoxythymidine monophosphate or dTMP)

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27
Q

where does MTX MOA work?

A

inhibits dihydrofolate reductase (decreases dTMP)

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28
Q

where does trimethoprim (TMP) work?

A

inhibits bacterial dihydrofolate reductase (decreases dTMP)

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29
Q

What causes orotic aciduria?

A

inability to convert orotic acid to UMP bc defect in UMP synthase => UMP (de novo pyrimidine synthesis path)

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30
Q

What type of defect is UMP synthase?

A

bifunctional enzyme of autosomal recessive nature

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31
Q

what are the findings of orotic aciduria?

A

orotic acid in urine;
megaloblastic anemia (no improve w/ B12 or folate)
failure to thrive;
NO HYPERAMMONEMIA

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32
Q

Tx for orotic aciduria

A

oral uridine admin

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33
Q

differentiate orotic aciduria from OTC deficiency

A

orotic aciduria=> no hyperammonemia;

OTC deficiency=> increase orotic acid and hyperammonemia

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34
Q

Name enzyme and what is converted as a result of its presence within the purine salvage pathway

A

1) HGPRT + PRPP=> converts guanine to GMP; and hypoxanthine to IMP
2) APRT + PRPP => converts adenine to AMP
3) adenosine deaminase => converts adenosine to inosine
4) Xanthine oxidase=> converts hypoxanthine to xanthine and xanthine to uric acid

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35
Q

Adenosine deaminase deficiency results in what disease?

A

Severe combined immunodeficiency disease;

SCID

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36
Q

How does adenosine deaminase deficiency lead to SCID?

A

excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase => prevents DNA synthesis & decreases lymphocytes

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37
Q

An absence of HGPRT results in what disease?

A

Lesch-Nyhan syndrome

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38
Q

Define how Lesch-Nyhan syndrome’s absence of HGPRT leads to disease

A

XLR=> defective purine salvage results in excess uric acid production and de novo purine synthesis

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39
Q

Findings of Lesch-Nyhan syndrome

A

retardation, self-mutilation, aggression, hyperuricemia, gout, choreoathetosis

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40
Q

define unambiguous in genetic code

A

each codon specifies only 1 amino acid

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41
Q

define degenerate or redundant in genetic code

A

most amino acids are coded by multiple codons

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42
Q

What are the exceptions of degenerate / redundant principles in the genetic code?

A

methionine (AUG) and tryptophan (UGG) encoded by only 1 codon

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43
Q

define the principle of commaless, nonoverlapping genetic code features

A

read from a fixed starting point as a continous sequence of bases

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44
Q

what are the exceptions to commaless, nonoverlapping features of genetic code?

A

some viruses

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45
Q

define principle of universal features to genetic code and what is the exception?

A

genetic code is conserved throughout evolution;

human mitochondria

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46
Q

give in order the severity of damage in point mutations in DNA (least to worst)

A

silent < missense < nonsense < framshift

47
Q

define silent DNA point mutation

A

same position amino acid, often base change in 3rd position of codon => tRNA wobble

48
Q

define missense DNA point mutation

A

changed amino acid (conservative-new amino acid is similar in chemical structure)

49
Q

define nonsense DNA point mutation

A

change resulting in early STOP codon

50
Q

define frameshift DNA point mutation

A

change resulting in misreading of all nucleotides downstream => truncated, nonfunctional protein

51
Q

Describe DNA replication in eukaryotes and important in the synthesis

A

replication is semiconservative and involves both continuous and discontinuous (Okazaki fragment) synthesis

52
Q

What is significant about the difference of origin of replication in prokaryotes and eukaryotes?

A

single => prokaryotes
multiple=> eukaryotes

sequence of base pairs in genome where DNA replication begins

53
Q

define replication fork

A

Y shaped region along DNA template where leading and lagging strands are synthesized

54
Q

define helicase

A

unwinds DNA template at replication fork

55
Q

define single-stranded binding proteins

A

prevent strands from reannealing

56
Q

define DNA topoisomerases

A

create a nick in helix to relieve supercoils created during replication

57
Q

What Rx attacks the DNA topoisomerases of prokaryote?

A

Fluoroquinolones => inhibit DNA gyrase;

prokaryotic topoisomerase II

58
Q

define primase

A

makes RNA primer on which DNA polymerase III can initiate replication (prokaryote)

59
Q

Define DNA polymerase III (prokaryotic only)

A

elongates leading strand by adding deoxynucleotides to 3’ end;
elongates lagging strand until reaches primer of preceding fragment

60
Q

define synthesis and proofreading activity of DNA polymerase III

A

5’-3’ synthesis;

proofreads w/ 3’-5’ exonuclease

61
Q

what is role of DNA polymerase I (prokaryotic only)?

A

degrades & replaces RNA primer w/ DNA;

excises RNA primer w/ 5’-3’ exonuclease

62
Q

role of DNA ligase

A

catalyzes formation of phosphodiesterase bond w/in strand of double stranded DNA => seals Okazaki fragments

63
Q

role of telomerase

A

enzyme adds DNA to 3’ ends of chromosomes to avoid loss of genetic material w/ every duplication

64
Q

What are the single strand DNA repair vehicles?

A

nucleotide excision repair;
base excision repair;
mismatch repair

65
Q

Which is single strand DNA repair vehicle is mutated in xeroderma pigmentosum? how does it present?

A

nucleotide excision repair;

prevents repair of pyrimidine dimers bc of UV light exposure

66
Q

What is the important DNA repair vehicle in repair of spontaneous/toxic deamination?

A

base excision repair

67
Q

What is DNA repair vehicle is mutated in HNPCC?

A

mismatch repair

68
Q

What is the double strand DNA repair vehicle? what is it mutated in?

A

nonhomologous end joining =>

mutated in ataxia telangiectasia

69
Q

What direction are DNA and RNA synthesized?

A

5’ ->3’

70
Q

what direction are proteins synthesized?

A

N terminus => C terminus

71
Q

When synthesizing DNA or RNA, what provides energy for the process?

A

1st nucleotide at the 5’ end provides triphosphate

72
Q

Where do many drugs blocking DNA replication try to modify?

A

triphosphate bond is target of 3’ hydroxyl attack to prevent addition of next nucleotide => chain termination

73
Q

What are the most abundant type of RNA? longest type? smallest type?

A

rRNA=> abundant type;
mRNA=> longest type;
tRNA=> smallest type

74
Q

mRNA start codon

A

AUG (eukaryotes=> methionine removed before complete translation)
(prokaryotes=> codes for formylmethionine (f-met)

75
Q

mRNA stop codons

A

UGA, UAA, UAG

76
Q

What is the direction of the sense strand in the gene?

A

5’=>3’

77
Q

what is direction of template strand in gene?

A

3’ => 5’

78
Q

role of promoter in gene expression

A

site where RNA polymerase & multiple other transcription factors bind to DNA upstream from gene locus

79
Q

what makes up the promoter site?

A

AT-rich upstream sequence w/ TATA and CAAT boxes

80
Q

what will a promoter mutation result in?

A

dramatic decrease in amount of gene transcribed

81
Q

what is enhancer in regulation of gene expression?

A

stretch of DNA that alters gene expression by binding transcription factors

82
Q

what is the silencer in gene expression?

A

site where negative regulators (repressors) bind

83
Q

What is unique about the enhancers and silencers of gene expression?

A

may be located close to, far from, or w/in an intron the gene whose expression it regulates

84
Q

in eukaryotes, what is the role of RNA polymerase I?

A

makes rRNA (most numerous RNA)

85
Q

in eukaryotes, what is the role of RNA polymerase II?

A 
makes mRNA (largest RNA);
opens DNA at promoter site
86
Q

in eukaryotes, what is the role of RNA polymerase III?

A

makes tRNA (smallest RNA)

87
Q

What is the proofreading vehicle in RNA polymerase?

A

there is no proofreading function of RNA but can initiate chains

88
Q

What is the role of RNA polymerase in prokaryotes?

A

1 RNA polymerase makes all 3 kinds of RNA

89
Q

A patient is known to have eaten mushrooms. what is the cause of the severe hepatotoxicity?

A

alpha-amantin from the Amanita phalloides (death cap mushrooms) => inhibits RNA polymerase II

90
Q

In RNA processing, what is the initial transcript?

A

heterogeneous nuclear RNA that becomes pre-mRNA

91
Q

Describe how RNA processing occurs

A

in nucleus after transcription

1) capping 5’ end
2) polyadenylation on 3’ end (poly-A tail-AAUAAA)
3) splicing out of introns

92
Q

what is required to get to mRNA?

A

capped, tailed, and spliced transcript => RNA processed before transported out of nucleus

93
Q

What do patients w/ lupus make antibodies to in RNA?

A

Abs to spliceosomal snRNPs

94
Q

give the splicing process of pre-mRNA

A

1) 1’ transcript combines w/ snRNPs and other proteins to form spliceosome
2) Lariat-shaped (looped) intermediate is generated
3) Lariat released to remove intron precisely and join 2 exons

95
Q

differentiate exons vs introns

A

exons contain actual genetic information coding for protein=> exons exit and expressed
introns intervening noncoding DNA segments => introns intervene and stay in nucleus

96
Q

what is the structure of tRNA?

A

secondary structure, cloverleaf form, anticodon end is opposite 3’ aminoacyl end;
CCA at 3’ along w/ high % of modified bases

97
Q

Why is aminoacyl-tRNA synthetase called the matchmaker?

A

scrutinizes AA before and after binding to tRNA and has the energy for formation of peptide bond

98
Q

What occurs if tRNA is mischarged?

A

reads usual codon but inserts wrong amino acid

99
Q

what is responsible for accuracy of amino acid selection?

A

aminoacyl-tRNA synthetase and binding of charged tRNA to codon

100
Q

Where does tetracyclines bind thus preventing what?

A

bind 30S subunit and prevent attachment of aminoacyl-tRNA

101
Q

describe the tRNA wobble

A

accurate base pairing required in 1st 2 nucleotide positions of mRNA codon so codons in 3rd wobble position code for tRNA/AA

102
Q

What activates the initiation of protein synthesis?

A

GTP hydrolysis and initiation factors help assemble 40S ribosomal subunit w/ initiator tRNA

103
Q

differentiate eukaryote ribosomal subunits w/ prokaryotic subunits

A

Eukaryotes: 40S and 60S -> 80S

Prokaryotes: 30S and 50S => 70S

104
Q

differentiate role of ATP from GTP in initiation process

A

ATP=> tRNA activation (charging);

GTP=> tRNA Gripping & Go places (translocation)

105
Q

describe the elongation process of protein synthesis

A

1) aminoacyl-tRNA binds to A site (except for initiator methionine)
2) ribosomal rRNA (ribozyme) catalyzes peptide bond formations, transfers growing polypeptide to AA in A site
3) ribosome advances 3 nucleotides toward 3’ end of mRNA moving peptidyl tRNA to P site (translocation)

106
Q

describe the termination of protein synthesis

A

stop codon recognized by release factor and completed protein released from ribosome

107
Q

where do aminoglycosides bind to block protein synthesis?

A

bind 30S and inhibit formation of initiation complex and cause misreading of mRNA

108
Q

where do tetracyclines bind to block protein synthesis?

A

bind 30S and block aminoacyl tRNA from entering acceptor site

109
Q

where do chloramphenicol bind to block protein synthesis?

A

binds 50S and inhibits peptidyl transferase

110
Q

where do macrolides bind to block protein synthesis?

A

bind 50S and prevent release of uncharged tRNA after it has donated its amino acid

111
Q

describe the trimming involved in post-translational modifications

A

removal of N- or C-terminal propeptides from zymogens to generate mature proteins

112
Q

describe the covalent alterations involved in post-translational modifications

A

phosphorylation, glycosylation, hydroxylation, methylation, and acetylation

113
Q

describe the proteasomal degradation involved in post-translational modifications

A

attachment of ubiquitin to defective proteins to tag them for breakdown

FA: Biochemistry (5 decks)

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