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Biochemistry-Nucleic acids > Introduction to Nucleic Acids > Flashcards

Introduction to Nucleic Acids Flashcards

1
Q

T or F: Information encoded in a DNA molecule is transcribed via
synthesis of an RNA molecule

A

True

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2
Q

T or F: The sequence of the RNA molecule is “read” and is translated into
the sequence of amino acids in a protein

A

True

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3
Q

The Central Dogma

A

a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein. Includes
Replication
Transcription
Translation

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4
Q
  1. Replication
A

Dna replication yields 2 molecules identical to the O.G one , ensuring transmission of genetic info. to daughter cells

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5
Q
  1. Transcription
A

It uses DNA as a template to make an RNA (mRNA) molecule. During transcription, a strand of mRNA is made that is complementary to a strand of DNA.Jul

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6
Q
  1. Translation
A

3-base codons on the mRNA corresponds to specific amino acids direct sequence of building a protein. Codons are recognized by tRNAs (transfer RNAs) carrying appropriate amino acids. Ribosomes are the “machinery” for protein synthesis

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7
Q

DNA stands for

A

Deoxyribonucleic Acid

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8
Q

RNA stands for

A

Ribonucleic acid

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9
Q

Nucleotides are composed of 3 things..

A

-A pentose sugar (Ribose or Deoxyribose)
-A nitrogenous base
-one phosphate group

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10
Q

Nucleosides are composed of

A

-Sugar and Base only

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11
Q

Pyrimidines include:

A
  1. Cytosine (C)
  2. Uracil (U) – RNA only
  3. Thymine (T) – DNA only
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12
Q

Pyrimidines form bonds to a…

A

5-C sugar via their N1 atoms

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13
Q

Purines include:

A
  1. Adenine (A)
  2. Guanine (G)
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14
Q

Purines form bonds to a

A

5-C sugar via their N9 atoms

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15
Q

The aromaticity and electron-rich nature of pyrimidines and purines enable them to
undergo

A

Keto-enol tautomerism

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16
Q

Tautomers

A

are isomers (constitutional isomers) of organic compounds that readily
interconvert by a chemical reaction called tautomerization

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17
Q

T or F:Protonation states of the nitrogens determines whether they can serve as H-bond donors or acceptors

A

True

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18
Q

T or F: Aromaticity also doesnt account for strong absorption of UV light

A

true

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19
Q

Primed numbers, indicate

A

Atoms in sugar

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20
Q

Non-primed numbers, indicate

A

atoms in base

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21
Q

phosphate group may be attached to the sugar at either of two positions

A
  • if at C3’, it is called a 3’ nucleotide
  • if at C5’, it is called a 5’ nucleotide
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22
Q

Importance of Nucleotides

A
  1. form polymers-Nucleic Acids
    * Functions are information storage and transfer
    * “Management for genetic information”
  2. Participate in Metabolic Reactions
    * ex: ATP
    * energy carrier/transfer agent
    * provides energy
    * FYI: Humans typically recycle their weight of ATP
    each day
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23
Q

how is the sequence read

A

always read 5’ to 3’

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24
Q

T or F: Phosphates in these polynucleotides are acidic (lose proton easily)

A

true

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25
Q

Polyanions

A

carry negative charges

26
Q

At physiological pH,nucleic acids are

A

polyanions

27
Q

pApUpCpG or pAUCG
“p” on left side of a nucleotide indicates

A

5’ phosphoryl group

28
Q

If deoxyribose (2’-H) then d(pATCG) “d” designates

A

Deoxy (slide 21)

29
Q

DNA is Important because:

A

contains genetic information

30
Q

RNA is important because:

A

makes protein base on instruction of DNA

31
Q

T or F: If RNA is damaged , it can’t be degraded and regenerated

A

False it can

32
Q

Why does DNA contain Thymine?

A

Because Cytosine deaminates to form uracil but repair enzymes recognize this as “mutations” and replace the Us w/C’s

33
Q

How would the repair enzymes distinguish natural U from mutant U?

A

Nature solves this by using Thymine (5methyl-u) in place of uracil

34
Q

Why is DNA 2’-deoxy and RNA is not?

A

-Vicinal OH groups (2’ and 3’) in RNA make it more susceptible to hydrolysis
-DNA lacking 2’OH is more stable
Genetic material must be more stable
RNA is designed to be used and then broken down

35
Q

Are Nucleic Acids Susceptible to Hydrolysis?

A
  • DNA is not susceptible to base
  • RNA is hydrolyzed by dilute base
36
Q

Know mechanism of Alkaline Hydrolysis of RNA

A

Draw it

37
Q

Nucleic Acid Structure: DNA and RNA

A

DNA- double helix
RNA- single stranded can form stem loop structures

38
Q

“Chargaff’s rules”

A

suggested that A&T bases pair together and that G&C bases pair together

39
Q

Base Pairs

A

A:T base pair has 2 hydrogen bonds
* G:C base pair has 3 hydrogen bonds

40
Q

Base Stacking

A

van der Waals interactions between
adjacent base pairs
* G:C-rich regions are more stable

41
Q

Palindromes

A

A special feature of DNA

42
Q

Why are Palindromes Important?

A

-Palindromes mark the beginning of a gene
-Palindromes mark the end of a gene
-Participate in control of gene function
-identify break points in DNA sequences (restriction enzymes)

43
Q

Different classes of Nucleic Acids? DNA

A

one type, one purpose

44
Q

Different classes of Nucleic Acids? RNA

A

*ribosomal RNA
* messenger RNA
* transfer RNA

45
Q
  1. messenger RNA (mRNA)
A

carries the message for protein synthesis

46
Q

2.ribosomal RNA (rRNA)

A

the basis of structure and function of ribosomes in translation of mRNA producing protein

47
Q

3.transfer RNA

A

carries the amino acids for protein synthesis

48
Q

RNA Structure

A
  • RNA primarily occurs as single strands
  • Can participate in base-pairing
  • A:U, G:C
  • Form stem-loop structures
49
Q

RNA Functions

A
  1. Bacterial Ribosomes
  2. Transfer RNA molecules (tRNAs)
  3. ribozymes- catalytically active RNA
50
Q

DNA structure

A

double helix, unique higher order structure that is stable, allows for access during replication and transcription

51
Q

The B-form of the DNA double helix…

A

the pitch (the distance
required to complete one helical turn) is 3.4 nm

52
Q

Histone Proteins

A

-are proteins
-5 major classes
1. H1
2. H2A
3. H2B
4. H3
5. H4
2-5 Amino acid sequence is conserved
* Histones are post-
translationally modified
and these modifications
are linked to transcriptional activation or silencing

53
Q

Nucleosomes

A

“beads on a string”
146 bp DNA- Histone core of nucleosome
55bp DNA - Linker DNA of Nucleosome

54
Q

Chromatin

A

complex of DNA and proteins that can condense into 30 nm fibers
* Two classes of chromatin: (1) Heterochromatin (condensed) and (2) euchromatin
(expanded)
which functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis, and to control gene
expression and DNA replication

55
Q

Heterochromatin (condensed)

A

-acetylation and methylation
Heterochromatin is silent for gene expression

56
Q

euchromatin
(expanded)

A

-deacetylation and de methylation
is active for gene expression

57
Q

Chromatin state is dictated by histone protein modifications

A

acetylation and methylation

58
Q

Chromosomes

A

composed of fibers of condensed chromatin that fold with protein scaffolds to form chromosomes

59
Q

Small nuclear RNAs (snRNA

A

associate with proteins forming small nuclear
ribonucleoprotein particles (snRNPs) and are involved in processing eukaryotic
gene transcripts into mature mRNA for transport to cytoplasm (where
transcription occurs in nucleus and translation occurs in cytoplasm

60
Q

Regulatory Roles

A

RNA molecules aid in regulating processes such as gene expression, chromatin organization, and programmed cell death

61
Q
A

Biochemistry-Nucleic acids (2 decks)

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