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2. wk > Struc of Nucleic Acids > Flashcards

Struc of Nucleic Acids Flashcards

1
Q

What are the functions of nucleotide?

A
  • Energy for metabolism (Stoffwechsel) (ATP)
  • Enzyme cofactors (NAD+)
  • Signal transduction (cAMP)
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2
Q

What are the functions of nucleic acid?

A
  • Storage of genetic info (DNA)
  • Transmission of genetic info (mRNA)
  • Processing of genetic information (ribozymes)
  • Protein synthesis (tRNA and rRNA)
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3
Q

What is metabolism?

A

-bezeichnet man die gesamten chemischen und physikalischen Vorgänge der Umwandlung chemischer Stoffe bzw. Substrate (z. B. Nahrungsmittel und Sauerstoff) in Zwischenprodukte (Metaboliten) und Endprodukte im Organismus von Lebewesen

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4
Q

What are Enzyme?

A
  • macromolecular biological catalysts
  • > accelerate chemical reactions
  • The molecules upon which enzymes may act are called substrates
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5
Q

What is signal transduction?

A
  • process of transferring a signal throughout an organism, especially across or through a cell
  • Signal transduction relies on proteins known as receptors, which wait for a chemical, physical, or electrical signal
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6
Q

How is a nucleotide structured?

A
  • Nitrogeneous base (organischen Base (Purin oder Pyrimidinbase) mit einem heterozyklischen Ring oder Ringsystem)
  • Pentose (a sugar)
  • Phosphate
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7
Q

What is a heterocyclic compound or ring structure?

A

-a cyclic compound that has atoms of at least two different elements as members of its ring(s)

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8
Q

How is a nucleoside structured?

A
  • Nitrogeneous base

- Pentose

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9
Q

How is a nucleobase structured?

A

-Nitrogeneous base

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10
Q

How is the phosphate group charged at neutral pH?

Where is it attached?

A

-Negatively charged at neutral pH
-Typically attached to 5’ position
-Nucleic acids are built using 5’-triphosphates
ATP, GTP, TTP, CTP
-Nucleic acids contain one phosphate moiety per nucleotide
-May be attached to other positions (5’; 2’; 3’; 2’, 3’)

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11
Q

Which forms does pentose have in nucleotides?

A
  • β-D-ribofuranose in RNA
  • β-2’-deoxy-D-ribofuranose in DNA (deoxy means without O in 2 carbon)
  • Different puckered conformations of the sugar ring are possible
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12
Q

Give some facts about Nucleobases (derivates, molecule, structure, absorption)

A
  • Derivatives of pyrimidine or purine
  • Nitrogen-containing heteroaromatic (O, N, S) molecules
  • Planar or almost planar structures (liegen auf einer ebene)
  • Absorb UV light around 250–270 nm
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13
Q

Name some base which are counted as pyrimidine bases+ name pKa

A
  • Cytosine is found in both DNA and RNA
  • Thymine is found only in DNA
  • Uracil is found only in RNA
  • All are good H-bond donors and acceptors
  • Cytosine pKa at N3 is 4.5
  • Thymine pKa at N3 is 9.5
  • Neutral molecules at pH 7
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14
Q

Draw the structure of cytosine, thymine and uracil

A

.

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15
Q

Name some base which are counted as purine bases+ name pKa

A
  • Adenine and guanine are found in both RNA and DNA
  • Also good H-bond donors and acceptors
  • Adenine pKa at N1 is 3.8
  • Guanine pKa at N7 is 2.4
  • Neutral molecules at pH 7
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16
Q

Draw the structure of adenine and guanine

A

.

17
Q

Where is the N-glycosidic bond attached in nucleotides?

A

-n nucleotides the pentose (Zucker) ring is attached to the nucleobase via N-glycosidic bond
-The bond is formed:
to position N1 (bottom right) in pyrimidines
to position N9 (bottom) in purines
-This bond is quite stable toward hydrolysis, especially in pyrimidines
-Bond cleavage is catalyzed by acid

18
Q

The UV absorption of Nucleobase is due to? (danger of genetic material?)

A
  • Absorption of UV light at 250–270 nm is due to π → π* electronic transitions
  • Excited states of common nucleobases decay rapidly via radiationless transitions
  • Effective photoprotection of genetic material
  • No fluorescence (spontaneous emission) from nucleic acids
19
Q

Give the nomenclature of nucleotide and Nucleic Acid

A
  • Nucleoside, Nucleotide, Nucleic acid
    -Purine:
    -Adenine: (Deoxy)Adenosine, (Deoxy)Adenylate, (DNA)RNA
    -Guanine: (Deoxy)Guanosine,
    (Deoxy)Guanylate, (DNA)RNA
    -Pyrimidines:
    -Cytosine: (Deoxy)Cytidine, (Deoxy)Cytidylate, (DNA)RNA
    -Thymine: Thymidine/(Deoxythymidine), (Deoxy)Thymidylate, DNA
    -Uracil: Uridine, Uridylate, RNA
    ———
    ribothymidine is used to describe its unusual occurrence in RNA
20
Q

Give structure, name and symbol of:

  • Deoxyadenylate
  • Deoxyguanylate
  • Deoxythymidylate
  • Deoxycytidylate

+draw them

A

-Deoxyadenylate (deoxyadenosine 5’- monophosphate) (A, dA, dAMP)
-Deoxyguanylate (deoxyguanosine 5’- monophosphate) (G, dG, dGMP)
-Deoxythymidylate (Deoxythymidine
5’- monophosphate) (T, dT, dTMP)
–Deoxycytidylate (deoxycytidine 5’- monophosphate) (C, dC, dCMP)

21
Q

Give structure, name and symbol of (Ribonucleotide):

  • adenylate
  • guanylate
  • uridylate
  • cytidylate

+draw them

A
  • adenylate (adenosine 5’- monophosphate) (A,AMP)
  • guanylate (guanosine 5’- monophosphate) (G, GMP)
  • Uridylate (uridine) (U, UMP)
  • Cytidylate (cytidine 5’- monophosphate) (C, CMP)
22
Q

What is use of epigenetic marker in prokaryotes and eukaryotes?

A
  • Way to mark own DNA so that cells can degrade foreign DNA (prokaryotes)
  • Way to mark which genes should be active (eukaryotes)
23
Q

Where is 5-Methylcytosine common? Where is N^6-Methyladenosine common?

A
  • in eukaryotes, also found in bacteria

- in bacteria, not found in eukaryotes

24
Q

Draw the structure of 5-Methycytidine, N^6-Methyladenosine, N^2-Methylguanosine, 5- Hydroxymethylcytidine

A

.

25
Q

Backbone polynucleotides; stability, directionality,

A 
-Covalent bonds formed via phosphodiester linkages
negatively charged backbone
 -DNA backbone is fairly stable:
Hydrolysis accelerated by enzymes (DNAse)
-RNA backbone is unstable:
In water, RNA lasts for a few years
In cells, mRNA is degraded in few hours
-directionality:
5’ end is different from 3’ end
We read the sequence from 5’ to 3’
26
Q

Linear polymers do not have?

A

-branching (verzweigungen) or cross-links (Querverbindungen)

27
Q

Describe the mechanism of Base-catalyzed RNA Hydrolysis

A
  • RNA hydrolysis occurs when the deprotonated 2’ OH of the ribose, acting as a nucleophile, attacks the adjacent phosphorus in the phosphodiester bond of the sugar-phosphate backbone of the RNA
  • > phosphorus is bonded to five oxygen atoms
  • ->The phosphorus then detaches from the oxygen connecting it to the adjacent sugar, resulting in ester cleavage of the RNA backbone
  • This produces a 2’,3’-cyclic phosphate that can then yield either a 2’- or a 3’-nucleotide when hydrolyzed
28
Q

Describe the hydrogen-bonding interactions

A
  • Two bases can hydrogen bond to form a base pair
  • For monomers, large number of base pairs is possible
  • In polynucleotide, only few possibilities exist
  • A pairs with T
  • C pairs with G
  • Purine pairs with pyrimidine
29
Q

What can you say about the difference between DNA strands?

A

-Two chains differ in sequence
(sequence is read from 5’ to 3’)
-Two chains are complementary
-Two chains run antiparallel

30
Q

Give a general description of RNA

A
  • Code Carrier for the Sequence of Proteins
  • Is synthesized using DNA template
  • Contains ribose instead of deoxyribose
  • Contains uracil instead of thymine
  • One mRNA may code for more than one protein
  • Together with transfer RNA (tRNA) transfers genetic information from DNA to proteins
31
Q

What happens with the bodes in DNA Denaturation? How can it be induced?

A
  • Covalent bonds remain intact
  • Genetic code remains intact
  • Hydrogen bonds are broken
  • Two strands separate
  • Base stacking is lost
  • > UV absorbance increases
  • induced by high temperature, or change in pH
  • -> denaturation may be reversible : annealing
32
Q

Describe there thermal DNA Denaturation (Melting)

A
  • DNA exists as double helix at normal temperatures
  • Two DNA strands dissociate at elevated temperatures
  • Two strands re-anneal when temperature is lowered
  • The reversible thermal denaturation and annealing form basis for the polymerase chain reaction (
33
Q

Name factors affecting DNA Denaturation

A
  • The midpoint of melting (Tm) depends on base composition
    • High CG increases Tm
  • Tm depends on DNA length
    • Longer DNA has higher Tm
    • Important for short DNA
  • Tm depends on pH and ionic strength
    • High salt increases Tm
34
Q

Why is the Denaturation of large DNA molecules

is not uniform ?

A

-AT rich regions melt at a lower temperature than GC-rich regions

2. wk (9 decks)

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