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Biochemistry Exam 2 > Chapter 9: Nucleic Acids > Flashcards

Chapter 9: Nucleic Acids Flashcards

1
Q
  • energy for metabolism (ATP)
  • enzyme cofactors (NAD+)
  • signal transduction (cAMP)
A

functions of nucleotides

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2
Q
  • storage of genetic info (DNA)
  • transmission of genetic info (mRNA)
  • processing of genetic information (ribozymes)
  • protein synthesis (tRNA and rRNA)
A

functions of nucleic acids

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3
Q

the order of bases on the polynucleotide sequence; the order of bases specifies the genetic code

A

primary nucleic acid structure

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4
Q

the 3-D conformation of the polynucleotide backbone

A

secondary nucleic acid structure

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5
Q

supercoiling

A

tertiary nucleic acid structure

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6
Q

interaction between DNA and proteins

A

Quaternary nucleic acid structure

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7
Q

a biopolymer containing three types of monomer untis

A

nucleic acid

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8
Q

What are the 3 types of monomer units found in nucleic acids?

A

1) a base derived from purine or pyrimidine (nucleobases)
2) a monosaccharide, either D-ribose or 2-deoxy-D-ribose
3) phosphoric acid

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9
Q

contains

  • nitrogenous base
  • pentose
  • phosphate
A

nucleotide

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10
Q

contains

  • nitrogenous base
  • pentose
A

nucleoside

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11
Q

contains

-nitrogenous base

A

nucleobase

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12
Q

What are some characteristics of nucleobases?

A
  • derivatives of pyrimidine or purine
  • nitrogen-containing heteroaromatic molecules
  • planar or almost planar structures
  • absorb UV light around 250-270nm
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13
Q

What are the pyrimidine bases?

-all are good H-bond donors and acceptors

A

Cytosine
Thymine
Uracil

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14
Q

Cytosine pKa at N3 is

A

4.5

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15
Q

Thymine pKa at N3 is

A

9.5

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16
Q

The pyrimidine bases are (uncharged/charged) at pH 7.

A

uncharged

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17
Q

What are the purine bases?

-also good H-bond donors and acceptors

A

Adenine

Guanine

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18
Q

Adenine pKa at N1 is

A

3.8

19
Q

Guanine pKa at N7 is

A

2.4

20
Q

The purine bases are (charged/uncharged) at pH 7.

A

uncharged

21
Q

describe characteristics of the b-N-glycosidic bond

A
  • in nucleotides the pentose ring is attached to the nucleobase via this bond
  • bond is formed to the anomeric carbon of the sugar in b configuration
  • the bond is formed to position N1 in pyrimidines and to position N9 in purines
  • bond is stable towards hydrolysis, especially in pyrimidines
  • bond cleavage catalyzed by acid
22
Q

Polynucleotides have covalent bonds formed via _____________ linkages.

A
  • phosphodiester linkages

- negatively charged backbone

23
Q

DNA backbone is _________ and RNA backbone is ________

A

stable; unstable

24
Q

We read the DNA/RNA sequence from which end to which end?

A

5’ to 3’ end

25
Q

The 2 strands are held together by _______, not by covalent bonds.

A

base-pairing hydrogen bonds
A-T
C-G

26
Q

the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule

A

primary DNA structure

27
Q

the ordered arrangement of nucleic acid strands

-double helix model: Watson and Crick in 1953

A

secondary DNA structure

28
Q

What is base stacking?

A

bases are hydrophobic and interact by hydrophobic interactions in standard B-DNA

29
Q

the 3-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling (further coiling and twisting of DNA helix)

A

tertiary DNA structure

30
Q

enzymes that change linking number of DNA are called ___________
-required for DNA unwinding and rewinding during transcription and replication

A

topoisomerases

31
Q

_____________ are targets for antibiotics and anti-cancer drugs

A

topoisomerases

32
Q

Describe the 2 types of topoisomerases.

A

Type 1: work by making cut in ONE DNA strand.

Type 2: work by making a cut in BOTH DNA strands

33
Q

Eukaryotic chromosomes are made of chromatin. What is it?

A

a filamentous complex of DNA, histones, and other non-histone proteins. It undergoes dramatic structural changes during cell division.
DNA binding to chromatin fosters the formation of supercoils.

34
Q

Histones bind tightly to DNA to form a structure called a ____________.

A

nucleosome

35
Q

What are some properties of histones?

A
  • small proteins
  • basic at neutral pH
  • positively charged
  • high percentage of Lys and Arg
  • binding to DNA induces the formation of supercoils
36
Q

_________ can be induced by high temperature or change in pH.

A

denaturation

37
Q

What are some characteristics of DNA denaturation?

A
  • covalent bonds remain intact (genetic code not disrupted)
  • hydrogen bonds are broken (two strands separate)
  • base stacking is lost (UV absorbance increases)
38
Q

What exactly is denaturation?

A

disruption of the secondary structure

39
Q
  • most commonly by heat denaturation
  • as strands separate, absorbance at 260nm increases (hyperchromicity)
  • midpoint of transition curve =Tm
  • higher % of G-C, the higher Tm
  • renaturation is possible on slow cooling
A

Characteristics of DNA denaturatuon

40
Q

What are some factors affecting DNA denaturation?

A
  • the midpoint of melting (Tm) depends on base composition
  • Tm depends on DNA length (longer DNA, higher Tm)
  • Tm depends on pH and ionic strength (high salt increases Tm)
41
Q

A-T rich regions melt at (higher/lower) temperatures than G-C rich regions.

A

lower

42
Q

transports amino acids to site of protein synthesis

A

Transfer RNA

43
Q

combines with proteins to form ribosomes, the site of protein synthesis

A

Ribosomal RNA

44
Q

directs amino acid sequence of proteins

A

Messenger RNA

Biochemistry Exam 2 (5 decks)

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