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Biochem > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

difference in DNA and RNA

A
  • presence or absence of oxygen at 2’ position
  • no O = DNA
  • O = RNA
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2
Q

pyrimidines

A
  • 6 membered heterocyclic rings of C and N

- heterocyclic

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3
Q

purines

A
  • fused 6 membered + 5 membered heterocyclic rings of C & N
  • heterocyclic
  • A and G
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4
Q

bases

A

N-groups can accept protons giving basic properties to molecule
-C and T and U

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5
Q

theobromine and theophylline

A
  • secondary metabolites of cocoa beans and tea leaves

- act as diuretic, cardiac stimulant, and vasodilator

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6
Q

caffeine

A
  • stimulant, diuretic

- antagonist to adenosine

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7
Q

nucleotide components

A
  • nitrogenous base
  • pentose sugar
  • phosphate
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8
Q

main components of nucleic acids

A

A,T,C,G, and U

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9
Q

Xanthine and hypoxanthine

A
  • rarely occur due to spontaneous deamination of G and A
  • removed during DNA repair
  • intermediates in nucleotide catabolism
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10
Q

uracil

A

occurs in RNA where it replaces T

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11
Q

free bases

A

poorly soluble, rarely occur

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12
Q

nucleosides

A
  • nitrogenous bases attached to sugars
  • sugar is either ribose or deoxyribose
  • rotation about glycosidic bond is possible
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13
Q

syn vs anti configurations of nucleosides

A
  • rotation about glycosidic bond results in syn and anti configuration
  • anti configuration favored
  • pyrimidines don’t form syn configuration bc steric hindrance between C2 oxygen and ribose ring
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14
Q

common ribonucleosides

A
  • cytidine
  • uridine
  • guanosine
  • adenosine
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15
Q

adenosine

A
  • physiologically active nucleoside
  • inhibitory neurotransmitter synthesized in brain
  • binds to adenosine receptors
  • binding causes drowsiness and vasodilation (allows more oxygen in during sleep)
  • accumulates during wakefulness
  • clinically used as anti-arrhythmic to defibrillate abnormally fast heart beats
  • caffeine competes with same receptor
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16
Q

cordycepin

A
  • physiologically active nucleoside
  • antibiotic produced by fungus
  • inhibits final step of RNA biosynthesis by termination of ribonucleotide chain due to absence of 3’ hydroxyl group
  • analog of adenosine
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17
Q

cytokinins

A
  • plant hormones derived from adenine
  • containe adenine ring system with an attached 5-carbon hydrophobic group at the free NH2
  • promotes cell division in plants
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18
Q

nucleotides

A
  • nucleosides with one or more phosphates

- base, sugar, and phosphate group

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19
Q

common ribonucleotides

A
  • adenosine-5’-monophosphate (AMP)
  • guanosine-5’-monophosphate (GMP)
  • cytidine-5’-monophosphate (CMP)
  • uridine-5’-monophosphate(UMP)
  • inosine-5’-monophosphate (IMP)
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20
Q

common deoxy-ribonucleotides

A
  • deoxyadenosine-5’-monophosphate (dAMP)
  • thymidine-5’-monophosphate (dTMP)
  • deoxyguanosine-5’-monophosphate (dGMP)
  • deoxycyctidine-5’-monophosphate (dCMP)
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21
Q

metabolic functions of nucleotides

A
  • building blocks of nucleic acids
  • atp
  • gtp
  • ctp
  • utp
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22
Q

atp

A
  • phosphate acceptor/donor in intermediary energy metabolism
  • biosynthetic processes
  • active transport
  • mechanical work (muscles)
  • temperature regulation
  • bioluminescence
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23
Q

gtp

A

protein synthesis and signal transduction

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24
Q

ctp

A

membrane and storage lipid synthesis

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25
Q

utp

A

carbohydrate synthesis and degradation

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26
Q

cyclic nucleotides

A
  • second messengers in signal cascades
  • relays a stimulus from an external first messenger
  • typically results in cascade of events leading to amplification of first messenger
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27
Q

first messenger

A

hormones, neurotransmitters

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28
Q

second messenger

A
  • Ca2+ ions
  • inositol-Pi3
  • diacylglycerol
  • cyclic nucleotides
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29
Q

cyclic amp

A
  • adenylate cyclase
  • ATP -> cAMP + PPi
  • cAMP involved in many signal cascades
  • hormone signaling
  • apoptosis
  • disease reactions
  • neuron function
30
Q

cyclic gmp

A
  • guanylate cyclase
  • GTP -> cGMP + PPi
  • cGMP is involved in nitric oxide (NO) signaling
  • blood pressure homeostasis
  • nerve impulse transmission
  • stress response in plants
31
Q

cAMP- mediated signal transduction

A
  • hormone binds to membrane receptor
  • GTP replaces GDP on inactive G protein on membrane
  • this converts G protein to active form
  • Active GTP-G protein complex activates adenylate cyclase
  • adenylate cyclase produces cAMP
  • cAMP activates protein kinase
  • protein kinase phosphorylates and inactive enzyme to convert it to active form
32
Q

flow of genetic info in a typical cell

A

replication (DNA) -> transcription (RNA) -> translation (protein)

33
Q

primary structure of nucleotides

A
  • sequence of nucleotides

- strand has 5’ to 3’ direction

34
Q

secondary structure of nucleotides

A
  • 3D arrangements of nucleotide residues with respect to one another
  • short term folding interactions such as double helix
  • usually DNA
35
Q

tertiary structure of nucleotides

A
  • longer range 3D interactions
  • superhelical forms: overwinding and underwinding cruciforms
  • protein and DNA interactions
36
Q

structural characteristics of DNA

A
  • 2 linear polynucleotide strands wound around each other to form double helix ladder
  • DNA has a rise. if DNA were a spiral staircase, the rise would be the distance from one step to the next
  • nucleotide monomers are composed of nitrogenous base, 2-deoxyribose sugar, phosphate group
  • sugar phosphates form background
  • bases form steps of ladder
  • strands are antiparallel
  • strands are held together via H bonding between bases
  • A and T form double bonds
  • C and G form triple bonds
37
Q

base pairing in DNA

A
  • purine ALWAYS pairs with pyrimidine
  • A always pairs w T (2 H bonds)
  • C always pairs w G (3 H bonds)
  • H bond distances relatively constant
  • paired bases in same plane
  • paired bases have same total distance across
38
Q

transcriptome

A

complete set of RNA molecules produced by a cell, tissue, or organism under specific physiological conditions

39
Q

proteome

A

complete set of protein molecules produced by a cell, tissue, or organism under specific physiological conditions

40
Q

metabolome

A

complete set of organic metabolites (sugars, lipids, amino acids) and macromolecules produced by a cell, tissue, or organism under specific physiological conditions

41
Q

hershey and chase

A
  • showed that DNA transferred from a virus to a bacterium contains sufficient info to direct synthesis of new virus
  • DNA has a high phosphorous content so used p32 labels
  • Proteins have lots of sulfur in them so they also used s35 labels
  • Allowed phage to infect E. Coli
  • Everything that had S35 did not infect bacteria
  • but phosphorous was incorporated in next generation
42
Q

chargaff

A
  • Found that all organisms had a fairly equal amount of A ant T and G and C
  • Hypothesized that A paired with T and G paired with C
  • Created Chargaff’s Rules!
43
Q

chargaff’s rules

A
  1. base composition of DNA varies from one species to the next
  2. DNA specimens from different tissues of same organism have same base components
  3. base composition of DNA in a given species doesn’t change with age, nutritional state, or environment
  4. in all cellular DNA molecules, A=T and G=C in concentration/number
44
Q

Watson and Crick

A

-double helix structure of DNA

45
Q

rosalind franklin

A
  • x-ray fiber diffraction

- helped determine double helix structure

46
Q

B-DNA spatial dimensions

A
  • individual helices not equally spaced (form major and minor grooves)
  • helices are right-handed
  • double helix makes one complete turn every 3.4 nm
  • 10.5 base pairs per turn.
  • essentially no linear space between base pairs
  • angle of base plane with ribose plane is perpendicular
  • form characterized by watson and crick
47
Q

A-DNA

A
  • observed when DNA is extracted from ethanol
  • more compact than B-form bc dehydrated
  • angle of base plane with ribose plane no longer perpendicular
48
Q

functions of major groove

A
  • recognition sites for several transcription initiation factors
  • specific domains of initiation factors lie here
  • promote separation of DA strands
  • allows proteins to interact with DNA
49
Q

functions of minor groove

A
  • not really known
  • often bind smaller (non-protein) ligands, which then can have several effects:
    1. inhibits some cancers
    2. inhibits topoisomerases
    3. antimicrobial activity
50
Q

stabilizing forces in DNA

A
  1. hydrogen bonds between base pairs
  2. hydrophobic interactions between bases and H2o
  3. van der waals forces
  4. electrostatic interactions
51
Q

hydrogen bonds between base pairs

A
  • 2 between AT pairs
  • 3 between CG pairs
  • maintain correct complementary orientation (no slipping)
  • have “zippering” effects (can sequentially form/separate)
  • AT pairs separate easier than CG pairs
52
Q

hydrophobic interactions between bases and H2o

A
  • purine and pyrimidine bases are non-polar
  • bases attract each other towards center of double helix while repelling/excluding water
  • phosphates are at surface attracted towards water
53
Q

van der waals forces

A
  • flat/planar bases can stack closer together

- cumulative effect of van der Waals forces become significant

54
Q

electrostatic interactions

A
  • sugar-phosphate backbone has negatively charged phosphate groups (destabilizing via repulsions)
  • repulsions are avoided by shielding
  • charges improve solubility in h2o
55
Q

Z-DNA structure

A
  • zig zag appearance
  • occurs in regions rich in alternating CGCG sequences
  • left handed
  • more elongated than B-DNA
  • syn orientation
56
Q

Z-DNA formation

A
  • not completely known
  • can occur at stretches of DNA with alternating G and C bases
  • small amounts form in cell when DNA is transcribed
  • may be important for controlling DNA replication
  • a family of conserved Z-DNA binding proteins exists
  • some viruses have Z-DNA binding domains-required for viral pathogenesis
57
Q

cruciform DNA

A
  • cross-like DNA structures that form when DNA contains a palindrome
  • one-half of the palindrome in one strand is complementary to the other half
  • double stranded region of palindrome separates
  • single strands fold upon themselves to base pair in complementary regions
  • cruciform DNA thought to be involved in protein binding to DNA
  • palindromes also serve as recognition sites for restriction enzymes
58
Q

triple stranded DNA

A
  • discovered in 1957
  • thought to form from partially unwound duplex DNA under “super-helical” conformational stress
  • polypyrimidine segment folds back to interact with polypurine region of remaining duplex forming triplex
  • third strand occupies major groove of original duplex
  • possible role in reonmbination
  • cannot be replicated! might have a role in preventing cancer
  • 3rd strand is parallel to purine strand
59
Q

linear dna

A

occurs in eukaryotic interphase chromosomes

60
Q

circular dna

A

occurs in prokaryotic chromosomes, plasmids, chloroplasts, and mitochondria

61
Q

super-coiled DNA

A
  • maximal in eukaryotic metaphase chromsomes
  • intermediate levels in prokaryotes and eukaryotes
  • compacts DNA to occupy less space
  • inaccessible (prevents replication and transcription)
  • protects DNA when not being replicated or transcribed
  • max coiling found in eukaryotic metaphase chromosomes during division
62
Q

snRNA

A

involved in removing introns and splicing exons together to form functional mRNA

63
Q

snoRNA

A

process rRNA, involved in ribosome biogenesis

64
Q

siRNA

A

-involved in gene silencing and regulation

65
Q

gRNA

A
  • needed for RNA editing

- removal and insertion of bases into mRNA

66
Q

tmRNA

A

disengages ribosomes from stalled translation of mRNA in bacteria

67
Q

telomerase RNA

A

forms much of structure and all of template required by telomerase

68
Q

hnRNA

A

function not really known (heterogeneous and nuclear RNA)

69
Q

tRNA structure

A
  • bases consistently occur in same positions
  • 3’ end: amino acid attachment
  • D loop: aminoacyl-tRNA synthetase recognition
  • TYC loop: ribosome recognition binding
  • anticodon loop: matching codon on mRNA during translation
70
Q

tRNA function

A
  • carry transfer amino acids to ribosome for assembly into polypeptides
  • at least one tRNA molecule for each of the 20 diff amino acids
  • anticodon base pairs with mRNA codons
  • often described as adaptor molecule

Biochem (12 decks)

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