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MCP Unit 2 > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

1868

A

-Miescher discovered nuclein from pus

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2
Q

1920

A

-Griffith discovered transmission of pathogenicity in strep pneumoniae

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3
Q

1944

A

Avery led team-DNA is genetic material

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4
Q

1952

A

Hershey and Chase-phage T2 can transmit DNA into bacteria

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5
Q

1951

A

Chargaff showed base ratios in DNA and RNA

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6
Q

152

A

Rosalind Franklin collected X-ray diffracted images of DNA molecule

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7
Q

1953

A

Watson and Crick solved double helix

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8
Q

1953

A

Crick presented central dogma

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9
Q

1958

A

Meselson and Stahl showed DNA is semi-conservative

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10
Q

2001

A

first draft of sequence of human genome

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11
Q

central dogma

A
  • DNA to RNA to protein

- DNA is two antiparallel strands linked together through H bonds

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12
Q

sense strand

A

carries coded genetic information

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13
Q

antisense strand

A

complementary sequence of bases oriented in opposite direction
-template for mRNA

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14
Q

genome

A
  • all hereditary material

- can be dsDNA, ssDNA, dsRNA, ssRNA

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15
Q

dsDNA

A
  • herpes, smallpox, papilloma,

- Hep B (retro and uses RNA in replication)

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16
Q

ssDNA

A
  • Bacteriphage, Parvovirus B19

- no DNA repair process- high rate of mutations- may be needed to adapt

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17
Q

dsRNA

A

-Rotavirus

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18
Q

ssRNA

A
  • plus sense- Hep C, Dengue, Rubella
  • minus sense- Measles, Mumps, Influenza
  • no repair- higher mutation rate
  • HIV- but needs DNA in replication
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19
Q

DNA vs RNA sugar

A

DNA lacks and OH on carbon 2

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20
Q

nucleoside

A

-sugar and base, no phosphate

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21
Q

phosphodiester bonds

A

-between 3’ and 5’ of sugar- strand runs 5-3

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22
Q

Pyrimidines

A
  • smaller
  • cytosine, thymine, uracil
  • cytosine to uracil loses amine
  • thymine to uracil loses methyl
  • flat planar 6-membered ring with two nitrogens
  • bond to sugar/phosphate is 1-sugar to 1-pyrimidine (bottom N)
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23
Q

Purines

A
  • bigger
  • Adenine and Guanine
  • flat planar 6-member ring fused to a 5 member ring with two nitrogens in each
  • 1-sugar to 9 purine (bottom N on 5 member ring)
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24
Q

Adenine

A
  • nucleoside is Adenosine

- NMP is Adenylate (AMP_

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25
Q

Guanine

A
  • Guanosine

- Guanylate (GMP)

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26
Q

Cytosine

A
  • Cytidine

- CMP-Cytidylate

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27
Q

Uracil

A
  • Uridine

- UMP- Uridylate

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28
Q

Thymine

A
  • Thymidine

- Thymidylate

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29
Q

Nucleotide

A
  • NMP or dNMP

- nucleoside and 1 phosphate

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30
Q

Nucleoside diphosphate

A
  • NDP of dNDP

- nucleoside and 2 phosphates

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31
Q

Nucleoside triphosphate

A
  • NTP or dNTP
  • nucleoside and 3 phosphates
  • immediate precursors for RNA or DNA synthesis
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32
Q

5-methyl-cytosine

A
  • influences packaging of chromosomal DNA

- important for X chromosome inactivations

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33
Q

5-hydroxylmethylcytosine

A

-may regulate gene expression by inducing DNA demethylation, found at high level in CNS

34
Q

Hypoxanthine

A
  • found int anticodon of tRNA, also used in purine biosynthesis
35
Q

Pseudouracil

A

-found in tRNAs

36
Q

N6-methyladenosine

A

-found in mRNAs and may affect gene expression and splicing

37
Q

nucleotide synthesis

A
  • can be de novo or salvage
  • de novo-synthesized from simpler starting materials, including amino acids. needs ATP hydrolysis
  • salvage-base reattached to ribose in activated form called PRPP
  • both pathways lead to synthesis of ribonucleotides first- RNA before DNA in evolution
38
Q

de novo synthesis of pyrimadines

A
  • orotic acid plus sugar–>UMP–>CMP and TMP

- framework for base first then attached to ribose

39
Q

de novo purine synthesis 1

A
  • sugar + purine ring synthesis–>IMP (from hypoxanthine) –> AMP and GMP
  • sugar first base added piece by piece
40
Q

de novo purine synthesis 2

A
  • PRPP (activated sugar) provides foundation on which bases on constructed
  • ring for purine from 10 step process that leads to formation of IMP. N comes from aa
  • IMP is branch point for AMP or GMP
  • IMP to GMP needs ATP (inhibited byGMP)
  • IMP to AMP needs GTP and aspartic acid (inhibited by AMP)
  • nucleoside monophosphate converted to di and tri through kinase activity
  • nucleoside diphosphates are reduced to deoxyrobonucleotides
41
Q

reduction reaction requires

A
  • thioredoxin reductase
  • ribonucleotide reductase
  • thioredoxin
42
Q

10-formyl-tetrahydrofolate

A
  • two steps in purine biosynthesis
  • one product is tetrahydrofolate- regenerates 10-formyl
  • tetrahydrofolate can be depleted by thymidylate synthase in synthesis of dTMP from dUMP, but is regenerated by dyhydrofolate reductase (DHFR) (from dihydrofolate)
  • if tetrahydrofolate isn’t regenerated, no de novo synthesis of purines or pyrimidines
  • dTMP pathway for cancer therapy because cancer cells consume dTMP-block thymidylate synthase with fluorodroxyuridylate
  • DHFR block- no tetrahydrofolate, no synthesis, no growth

**See picture

43
Q

purine salvage pathways

A
  • pre made bases
  • adenine + PRPP—> adenylate (AMP) +PPi-adenine phosphoribosyltransferase

-Guanine + PRPP—> guanylate (GMP) +PPi
-Hypoxanthine + PRPP—> inosinate (IMP) +PPi
^both hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

-can then form NDP, NTP, dNDP, dNTP

44
Q

nucleic acid catabolism

A
  • bases and NMP can be interconverted by phosphoribosyltransferase in presence of 5-phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP)
  • mononucleotides (NMPs) can go to NTPs and DNA, nucleosides, or nucleobases (T,C)
  • all purine degradation leads to uric acid which is excreted into urine as insoluble crystals
  • further breakdown to allantoin, allantoic acid, ammonia
  • ingested nucleic acids broken down by pancreatic nucleases and intestinal phosphodiesterases
45
Q

metabolism pathways in humans

A

-look at pg 20

46
Q

ADA

A

adenosine deaminase

47
Q

APRT

A

adenine phosphoribosyltransferase

48
Q

HPRT

A

hypoxanthine-guanine phosphoribosyltransferase

49
Q

NP

A

nucleoside phosphorylase

50
Q

5’ NT

A

5’ nucleotidase

51
Q

PAT

A

PRPP amidotransferase

52
Q

PRPP

A

phosphoribosylphosphate

53
Q

PRPPS

A

PRPP synthetase

54
Q

XO

A

xanthin oxidase

55
Q

gout

A
  • defects in PRPP synthetase and HGPRT
  • uric acid crystals precipitate into joints, kidneys, and ureters
  • treatment with xanthine oxidase inhibitors
  • lead impairs uric acid secretion
56
Q

Lesch-Nyhan sydrome

A
  • rare inherited disorder
  • deficiency of HGPRT
  • causes increased level of hypoxanthine and guanine (increased degradation of uric acid)
  • causes accumulation of PRPP and stimulates production of purine nucleotides
  • causes gout like symptoms, but also neurological symptoms
  • first neuropsychiatric abnormality attributed to a single enzyme
57
Q

cellular functions of nucleotides

A
  • building blocks for nucleic acid polymers, DNA, RNA
  • energy carriers
  • important components of co-enzymes: FAD, NAD(P)+ and coA
  • precursors for second messengers-c/gAMP (cAMP-AMP lose caffeine jolt)
  • activated intermediates in many biosynthetic pathways-S-adenosylmethionine (SAM) as methyl donor
58
Q

Base pairing and H bonds

A
  • 2 for AT and 3 for GC

- antiparallel

59
Q

B-DNA conformation

A
  • most common
  • right handed helix
  • plane of base is perpendicular to the SP backbone
  • 1 turn is 10.5 bp, 34 angstroms, 3.4 nm
  • major and minor grooves
  • antiparallel
  • repeating unit is 1 bp
60
Q

A-DNA

A
  • right handed
  • repeating unit is 1 bp
  • 11 bp per turn, 28 angstroms
  • appears in dehydrated samples
61
Q

additional conformations of DNA

A
  • favored by certain base sequences, salt conditions, base modifications, and humidity
  • single helix can contain A, B, and Z conformations
62
Q

Z-DNA

A
  • left handed
  • repeating unit is 2 bp
  • 12 bp/turn, 45 angstroms
  • not favorable
  • alternating purine/pyrimidine, neg supercoiling, high salt can induce Z formation
63
Q

DNA bending

A
  • facilitates protein-DNA interactions
  • larger major groove and smaller minor groove
  • proteins interact with side groups of a bp
  • each individual bp deviates from B conformation (depending on surrounding bases)-how binding proteins recognize- then alter more for other proteins
  • covalent mod-affect structure and binding
64
Q

hoogsten bp

A
  • purine bases can flip from normal anti conformation to a syn conformation and form different set of H bonds with pyrimidine partners
  • 1% of the time these bp exist in canonical duplex DNA
  • proteins probably recognize altered structure
  • another layer of gene regulation
65
Q

tm

A
  • melting temp
  • half dsDNA molecules dissociate into ssDNA
  • determined by size, GC content, salt concentration (high stabilizes), pH, other reagents
  • cloning, southern blot, FISH, microarrays, PCR
  • increase temp, pH, lower salt to melt DNA
  • lower GC content easier to melt
  • other reagents that can H bond with single stranded DNA stabilize it and decrease Tm
66
Q

denatured DNA

A
  • can be renatured and reform correct H bonds

- slow cooling allows complementary sequences to H bond

67
Q

complementary sequences

A

-single stranded sequences capable of H bonding with each other

68
Q

hybridization

A
  • ssDNA bound to nylon or a glass microchip can still renature with complementary strand
  • high or low stringency
69
Q

high stringency

A

at or close to Tm- only perfect matches can form

70
Q

low stringency

A

below Tm- under conditions that stabilize double helix- imperfect bp can form

71
Q

properties of chromosomal DNA

A
  • each chromosome is single long polymer of DNA
  • can be linear or circular
  • GC content varies in different organisms (humans~40%) and varies non-randomly along human chromosomes (telomeres GC rich, centromeres AT rich)
  • highly condensed DNA
  • degree of condensation varies during cell cycle and along length of chromosome
72
Q

topological stresss

A
  • supercoiling
  • positive is overwound, negative is underwound
  • cut by topoisomerases during replication or transcription to relieve stress
  • type I cuts 1 strand type II cuts both strands
73
Q

structural features of RNA

A
  • single stranded
  • shorter than DNA
  • complex tertiary structure
  • unstable-vulnerable to base-catalyzed hydrolysis at 2’ hydroxyl
  • pH above 7 RNA is degraded
  • can for intramolecular H bonded bp-hairpin and stem loop
  • secondary structure allows for well-defined shape that can be important for function and recognition-tRNA and ribozymes
74
Q

mRNA

A
  • 5% of total RNA, most heterogeneous in size of RNA types

- contains genetic info copied from specific regions of DNA to be used as a template for protein synthesis

75
Q

ncRNA

A
  • non-coding

- included miRNA, ribozymes

76
Q

rRNA

A
  • 80% of total RNA

- several species of distinct sized that are part of the structure of the ribosome

77
Q

tRNA

A
  • 15% of total RNA
  • small RNA - 73-93 nucleotides
  • contain elaborate secondary structures and some unique nucleotides
  • serve as adaptor molecules in protein synthesis-recognize the code in mRNA indicating which aa comes next in a protein and bring that aa to the site of protein synthesis on ribosome
  • have at least on specific tRNA molecule for each of the 20 aa
78
Q

miRNA

A
  • small endogenous RNA of 22 nt that play important regulatory roles in animal development
  • bind to complementary sites of specific mRNA to inhibit their translation
79
Q

siRNA

A
  • small interfering
  • 20-25bp dsRNA
  • function in RNA interference pathway
80
Q

ribozymes

A

-have elaborate secondary structure, which can form an active site that can catalyze intramolecular reactions and reactions with other RNA molecules much in the same way as enzymes

MCP Unit 2 (10 decks)

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