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Biochemistry > Nucleic Acid > Flashcards

Nucleic Acid Flashcards

1
Q

Nucleotides are linked by ……. bond, between the …… of one sugar and the …… of an adjacent sugar

A

phosphodiester bonds

3-OH , 5-phosphate ester

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2
Q

DNA exists as ……., with …… interactions between the …. & …. in the opposite strands

A

double helix
non covalent
purine, pyrimidine

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3
Q

The primary structure of DNA or RNA refers to ……..

Higher orders are linked by …… between purine and pyrimidine bases

A

sequence of nucleotides in DNA and RNA

non covalent bonds

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4
Q

Nucleotides consist of 3 parts: … , …. & ….

A

nitrogen base, pentose & phosphate group

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5
Q

The linkage of the nitrogen base to the pentose forms ……, the addition of phosphate forms ….

A

nucleoside, nucleotide

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6
Q

What are the types of nitrogenous bases?

A
  1. Purines: two rings with nitrogen atoms. two types, Adenine A & guanine G
  2. Pyrimidine: single ring with nitrogen. three types: cytosine C, thymine T (only in DNA) & uracile U (only in RNA)
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7
Q

RNA contains …. sugar, while DNA contains …. . The difference is …….

A

ribose, deoxyribose

deoxyribose has a hydrogen atom instead of hydroxyl attached to carbon 2

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8
Q

Phosphate groups are linked to pentose by …..

A

ester linkage to carbon 5

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9
Q

What are the types of phosphodiester links in nucleic acid?

A

3’-5’ phosphodiester linkage: most common in DNA and RNA
2’-5’ phosphodiester linkage: involved in RNA splicing
5’-5’ phosphodiester linkage: found in cap structure at the 5’ end of eukaryotic mRNA

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10
Q

Nucleotides have polarity. T/F

A

True

at one end there is a free 3’ hydroxyl group, at the other end there is a 5’ phosphate group

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11
Q

What are the differences between DNA and RNA?

A
  1. pentose: DNA has 2’-deoxyribose, while RNA has a ribose
  2. DNA is double stranded, while RNA is single
  3. DNA has G,A,C,T . . While RNA has G,A,C,U
  4. DNA is a repository for genetic information. While RNA is a working copy of DNA (transfers genetic information to protein sequences)
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12
Q

In purines, the ….. of the ring system is linked to carbon 1 on sugar, while in pyrimidines the …. of the ring is linked to carbon 1

A

nitrogen 9

nitrogen 1

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13
Q

The secondary structure for DNA is ……, while for RNA is …..

A

double stranded structure

the single strand can bend back on itself

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14
Q

The sugar is connected to the base by ….. bond, while one sugar to another is connected by ….

A

glycosidic

phosphodiester

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15
Q

Double structure can occur between ….., …. & ….

A
  1. DNA double helix
  2. single stranded RNA (bent on itself)
  3. RNA and DNA complementary to each other
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16
Q

The double DNA strands always run in ……. fashion

A

antiparallel

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17
Q

G-C bonds provide more stability to DNA than A-T & A-U because…..

A

G-C is connected by 3 hydrogen bonds, while the others by two

18
Q

Hydrophobic interactions occur between adjacent ….. & …… add stability to the double helix

A

pyrimidines and purines

* This is called base stacking

19
Q

Base stacking is interrupted by …….

A

intercalating agents, like Actinomycin D, which prevents replication (DNA-DNA) and transcription (DNA-mRNA)

20
Q

Nucleases enzymes cut …….. . Exonucleases remove ……., while endonucleases cut …..

A

the phosphodiester bonds
terminal nucleotides
between internal nucleotides

21
Q

Most DNA forms ………

A

right handed, antiparallel helix

22
Q

Define B DNA

A

is the typical right handed, anti-parallel double stranded, with the bases stacked and perpendicular to the axis of the helix. The helix has two grooves that provide site for DNA-protein interactions
* Also called Watson-Crick model

23
Q

Define Z DNA

A

Left handed, anti parallel helix. Usually rich with G-C sequences.
* It is a rare form with the function unknown

24
Q

Define A DNA

A

Resembles B DNA. but the bases are not perpendicular but tilted to axis.

  • This is the anhydrous type on B DNA
  • Found in DNA-RNA hybrids
25
Q

Circular DNA has no ….. so it resists ….. actions. It may be in relaxed form or …..

A

ends, exonuclease

supercoiles form

26
Q

Supercoiling is important in ……

A

DNA packaging

27
Q

What is difference between positive and negative supercoiling?

A
  1. Negative: twist the helix in counter clock wise turns. DNA is usually negatively supercoiled. Occurs in both circular and stranded chromosomes
  2. Positive: DNA is twisted in the same direction as the double helix
28
Q

Define the topoisomerase enzymes

A

Relieve the tension caused by supercoiling during replication, by cutting the phosphodiester bonds in the double strands and then resealing

29
Q

Nucleotides are synthesized by ……. or …..

A
  1. salvage pathway: The preferred method of synthesis in adults
  2. de novo synthesis: occurs in rapidly dividing cells
30
Q

In de novo synthesis of nucleotides, the precursors are ………

A

amino acids, ammonia, bicarbonate, ribose-5-phosphate & THF

* THF acts as a methylating agent in nucleotides synthesis

31
Q

Deoxyribonucleotides are synthesized by reduction of ……, catalyzed by …., …. & ….

A

ribonucleoside diphosphates

* This reaction is catalyzed by NADPH, reductase & thioredoxin

32
Q

Purine is synthesized …… ribose-5-phosphate throughout the assembly, while pyrimidines are …….

A

attached to

completely assembled before attaching to ribose-5-phosphate

33
Q

The parent purine nucleotide is ……, while pyrimidines parent is …..

A

IMP: give rise to both AMP & GMP (they also exert inhibition on purine synthesis)
OMP: forms both UTP & CTP, while Thymidine nucleotides (for DNA) is synthesized by methylation of dUMP by THF. CTP & UTP inhibit pyrimidine synthesis

34
Q

Nucleotides are degraded by removal of …… & ….., while the amino group is removed as ….. by the action of ….. & …..

A

phosphate & pentose
ammonia
guanine deaminase & adenosine deaminase

35
Q

How is the purine degraded?

A

The ring can not be degraded. It is excreted as uric acid

36
Q

How is the pyrimidine degraded?

A

Thymidine: becomes butyrate

Uracil & cytosin: become beta-alanine

37
Q

Folate is needed for the formation of the nucelotides ….., ….. & …..

A

adenosine, guanine & thymidine

* folate deficiency affects many tissues with high mitotic activity

38
Q

The catabolism of nucleotides gives …… ATP

A

zero

39
Q

The intermediate in the synthesis of purines and pyrimidines is …….

A

5-phosphoribosyl-1-pyrophosphate

  • PRPP either converted to purine or
  • converted to orotic acid —>orotate monophosphate —->pyrimidine
40
Q

Uric acid is formed from …. degradation

A

Purine

* purine —-> Xanthine —–> uric acid , catalyzed by xanthine oxidase

41
Q

DNA and RNA are differentiated in the lab by ………..

A

Feulgen reaction, which is specific for deoxyribose

42
Q

A nucleosome consists of …….

A

DNA wrapped around a histone & held by ionic bonds
* Histone is composed of Arginine & Lysine (+ve charged due to the free amino group) that bonds to the -ve phosphate of DNA

Biochemistry (13 decks)

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