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BCH 4024 Exam 1 > Lecture 3: Nucleic Acids > Flashcards

Lecture 3: Nucleic Acids Flashcards

1
Q

Chemical name for 1 phosphate?

Label the structure!

A

Monophosphate

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2
Q

Monomeric units w/ phosphates?

A

Nucleotides

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3
Q

Monomeric units that lack phosphates

A

Nucleosides

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4
Q

Label the Nucleotide!

How would it be different for DNA vs RNA?

A
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5
Q

Two ______ bases: DNA and RNA contain A & G.

A

Two Purine bases: DNA and RNA contain A & G.

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6
Q

Name the base.

A
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7
Q

Name the base.

A
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8
Q

3 _______ bases: DNA and RNA contain C;

mainly T in DNA;

mainly U in RNA.

A

3 Pyrimidine bases: DNA and RNA contain C;

mainly T in DNA;

mainly U in RNA.

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9
Q

Name the base.

A
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10
Q

Name the base.

DNA/RNA?

A

DNA

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11
Q

Name the base.

DNA/RNA?

A

RNA

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12
Q

Where does the Glycosidic Bond attach for Purines?

Pyrimidines?

A

Purines: At N9 to sugar at C1’

Pyrimidines: At N1 to sugar at C1

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13
Q

Name the Deoxyribonucleotide.

Symbols?

Nucleoside?

A
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14
Q

Name the Deoxyribonucleotide.

Symbols?

Nucleoside?

A
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15
Q

Name the Deoxyribonucleotide.

Symbols?

Nucleoside?

A
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16
Q

Name the Deoxyribonucleotide.

Symbols?

Nucleoside?

A
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17
Q

Name the Ribonucleotide.

Symbols?

Nucleoside?

A
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18
Q

Name the Ribonucleotide.

Symbols?

Nucleoside?

A
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19
Q

Name the Ribonucleotide.

Symbols?

Nucleoside?

A
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20
Q

Name the Ribonucleotide.

Symbols?

Nucleoside?

A
21
Q

What is this compound?

Nucleoside?

Nucleotides?

A

Adenosine Triphosphate

Nucleoside: Adenosine

Nucelotides: AMP, ADP, ATP

22
Q

Name the structure and phosphate.

A

Adenosine (Adenosine diphosphate, ADP)

Inorganic Phosphate

23
Q

Name the structure and phosphate.

A

Adenosine (Adenosine monophosphate, AMP)

Inorganic Pyrophosphate

24
Q

What types of substrates does DNA & RNA require?

A

dNTP, NTP

25
Q

DNA Secondary Structure was founded by whom and when?

A

Chargaff, 1950

26
Q

Chargaff’s Rules for DNA Secondary Structure:

  1. All ______ in the ______ species have the ___ mol-% of all _ nucleotides.
  2. mol-% of _____ = mol-% of _____
  3. %A = %___ and %G =%___
    • i.e. A+G =___+_____
  • W-C MODEL: A pairs w/ ___ and G pairs w/ ___, and same ____ in all cells
A

Chargaff’s Rules for DNA Secondary Structure:

  1. All tissues in the same species have the same mol-% of all 4 nucleotides.
  2. mol-% of Purines = mol-% of Pyrimidines
  3. %A = %T and %G =%C
    • i.e. A+G =T+C
  • W-C MODEL: A pairs w/ T and G pairs w/ C, and same DNA in all cells
27
Q

What is the backbone of DNA Secondary Structure according to Chargaff and where does new dNTP and NTP get added?

A

Phosphate-deoxyribose backbone

3’ end of growing polynucleotide chain

28
Q

According to the Watson-Crick Model, what type of backbone encompasses the nucleotides?

________ bases (paired by H-Bonding) on the inside – base-pairs are stacked on one another with planes ____ to the helix axis.

A

Hydrophilic phosphate-deoxyribose backbone

Hydrophobic bases (paired by H-Bonding) on the inside – base-pairs are stacked on one another with planes perpendicular to the helix axis.

29
Q

According to the Watson-Crick Model, complimentary strands run ________.

A-T has __ H-Bonds.

G-C has __ H-Bonds.

Which complimentary pair is is stronger?

A

According to the Watson-Crick Model, complimentary strands run antiparallel.

A-T has 2 H-Bonds.

G-C has 3 H-Bonds, hence the stronger bond.

30
Q

What form of DNA is a right-handed double helix, forms when fully hydrated and under conditions in vivo w. majority of proteins recognizing the major groove?

A

B-Form

31
Q

The B-form of DNA is a highly (+/-) molecule and every base needs __ phosphodiester bond(s).

A

The B-form of DNA is a highly - molecule and every base needs 1 phosphodiester bond.

32
Q

The B-form of DNA us a right-handed double helix model that is stabilized by:

  1. ________ interactions: base stacking
  2. __-Bonding between Pu—Py
  3. ______: neutralize the (-) on the phosphates along the helix of DNA
A

The B-form of DNA us a right-handed double helix model that is stabilized by:

  1. Hydrophobic interactions: base stacking
  2. H-Bonding between Pu—Py
  3. Cations: neutralize the (-) on the phosphates along the helix of DNA
33
Q

What form of DNA forms under dehydrated, non-physiological conditions; right-handed helix?

A

A-DNA

34
Q

What form of DNA is rich in GC content, left-handed, and is important in protein recognition & gene regulation?

A

Z-DNA

35
Q

Why does DNA need to be condensed and how does it fold?

A

To fit into cells, Linearly

36
Q

in eukaryotic cells, DNA is wrapped around proteins called ________ to help package it in cells.

A

in eukaryotic cells, DNA is wrapped around proteins called histones to help package it in cells.

37
Q

DNA bases can be modified to provide additonal level to the “code” = _______

A

DNA bases can be modified to provide additonal level to the “code” = epigenetics

38
Q

What is the loss of structure of DNA & proteins by melting w/ high heat, causing interaction of H-bonds and the chains to come apart?

A

Denaturation

39
Q

In what does the duplex melt (no covalent bonds break)?

  1. ?
  2. ?
  3. ?
A

In what does the duplex melt (no covalent bonds break)?

  1. Acid
  2. Alkali
  3. Heat
40
Q

Stability/melting temperature (Tm) a function of _/_ content because they contain _ H-bonds.

A

Stability/melting temperature a function of G/C content because they contain 3 H-bonds.

41
Q

What is the reassociation of denatured DNA strands?

And at what temp stability/melting temp is ideal?

A

Annealing

~25º C below Tm

42
Q

High ____ stabilizes the duplex, increasing Tm, due to

  • __________ interactions (bp’s)
  • ________ shielding
A

High salt stabilizes the duplex, increasing Tm, due to

  • Hydrophobic interactions (bp’s)
  • Phosphate shielding
43
Q

What determines the DNA and melting temperature (denaturation) for a molecule and why?

A

Amount of G/C content, due to the amount of H-bonds (3 in GC)

44
Q

What type of group is RNA secondary structure?

A

2’ OH group

45
Q

T/F: Does RNA have a simple, regular secondary structure?

A

False

46
Q

What are the most common secondary structures for RNA?

A

A-form double helices and hairpins

47
Q

Ribose 2’ OH of RNA causes _____ interactions in base stacking that prevent _____ of more than 10-12 bp’s.

A

Ribose 2’ OH of RNA causes steric interactions in base stacking that prevent coils of more than 10-12 bp’s.

48
Q

Steps of DNA duplication:

  1. ____ copies 3 nucleotide codon (_RNA)
  2. _RNA reads encoded gene information from _RNA
  3. _RNA transfers appropriate ____ ____ to a growing polypeptide chain for protein synthesis
A

Steps of DNA duplication:

  1. DNA copies 3 nucleotide codon (mRNA)
  2. tRNA reads encoded gene information from mRNA
  3. tRNA transfers appropriate amino acid to a growing polypeptide chain for protein synthesis

BCH 4024 Exam 1 (10 decks)

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