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Molecular Diagnostics > Nucleic acids structure and Mutations > Flashcards

Nucleic acids structure and Mutations Flashcards

lecture 2

1
Q

Mention the components of nucleic acid

A
  1. Phosphate groups
  2. Pentose sugar
  3. A nitrogenous base (purines including Adenine (A) and Guanine (G); and pyrimidines including Cytosine (C), Thiamine (T) and Uracil (U))
  4. RNA and DNA are two main nucleic acids
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2
Q

Define a nucleoside

A

A nucleoside a molecule is composed of a purine or pyrimidine base and a ribose or deoxyribose sugar

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2
Q

what is a nucleotide composed of

A

nucleotide is composed of nucleoside and phosphate group

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3
Q

5 functions of RNA

A
  1. Directs translation
  2. Ribosomal RNA have structural and enzymatic roles.
  3. Delivery of amino acids
  4. Participates in posttranscriptional processing
  5. Carrier of hereditary information in some viruses
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3
Q

Mention the 4 DNA stabilizing forces

A
  1. Sugar-phosphate chain conformation
  2. Base pairing using hydrogen bonds
  3. Base stacking and hydrophobic interactions
  4. Ionic interactions
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4
Q

What are the functions of DNA

A
  1. directs its own replication
  2. Direct the transcription of complementary RNA molecules
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5
Q

Define DNA mutation

A

The genotypic change as compared to the normal sequence

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6
Q

risk factors for DNA mutation

A
  1. Exposure to mutagenic agents like UV light, intercalating agents
  2. Errors in DNA replication and repair
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6
Q

Define polymorphism

A

Multiple forms of a gene or sequence variants with no obvious effect upon phenotype may be termed

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7
Q

under pont mutations, describe the other minor mtations under it

A
  1. Missense – results in a different amino acid
  2. Nonsense – results in stop codon hence termination of translation of the protein
  3. Silent - results in the same amino acid
  4. Transition - a purine replaced by a purine or a pyrimidine by a pyrimidine
  5. Transversion - a purine replaced by a pyrimidine or vice versa
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7
Q

Mention 2 types of mutations

A
  1. Point mutation
  2. Frameshift muatation
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8
Q

define frameshift mutation

A

The mutations that cause all of the subsequent three-letter codons to be changed

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9
Q

what does the cenral Dogma of biology states

A

The usual flow of genetic information is from DNA to mRNA to polypeptide

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9
Q

examples of frameshift mutation

A
  1. Deletions: involved loss of one or more nucleotides
  2. Insertion: involves the addition of one or more nucleotides into a gene
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9
Q

what are the two effects of mutations on proteins

A
  1. Loss-of-function: mutations can result in either reduced activity or complete loss of the gene product.
  2. Gain-of-function: mutations, result in either increased levels of gene expression or the development of a new function(s) of the gene product
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10
Q

Mention 6 enzymes that takes part in DNA replcation

A
  1. DNA topoisomerases
  2. Helicase
  3. RNA polymerase and primase
  4. Exonucleases
  5. Single strand binding proteins (SSBs)
  6. Ligases
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11
Q

what separates the two standed double helix of the DNA

A

DNA helicase

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12
Q

results of DNA replication

A

results in two daughter DNA duplexes that are identical to the original parent molecule

12
Q

the synthesis of complementary strands occurs in which direction

A

5′ to 3′ direction

12
Q

what directs DNA synthesis of a complementary DNA strand

A

DNA polymerases

13
Q

where does replication occur

A

replication bubble

13
Q

where does replication starts at

A

replication forks

14
Q

differentiate the synthesis of leading strand and lagging strad

A
  1. The leading strand, is synthesized continuously.
  2. The lagging strand, is synthesized in Okazaki fragments
14
Q

What direction does the DnaB protein translocate along the lagging strand template?

A

The DnaB protein translocates along the lagging strand template in the 5’ – 3’ direction.

15
Q

function of DNA ligase

A

Its primary function is to join DNA strands together by forming phosphodiester bonds between nucleotide

16
Q

Which direction do Rep helicase and PriA protein translocate along the DNA?

A

Rep helicase and PriA protein translocate along the DNA in the 3’ – 5’ direction.

16
Q

What is the role of Single Strand Binding proteins (SSB) in relation to the separated strand of the dsDNA?

A

Single Strand Binding proteins (SSB) bind the separated strand of the dsDNA to prevent reannealing

16
Q

What protective role do SSBs play regarding ssDNA?

A

SSBs protect the ssDNA from nucleases, which could degrade it.

16
Q

How do SSBs prevent the formation of secondary structures in ssDNA?

A

SSBs prevent ssDNAs from forming fortuitous intramolecular secondary structures by binding to them and stabilizing the single-stranded DNA

17
Q

How are SSBs removed from the ssDNA during DNA replication?

A

SSBs are stripped off the ssDNA by DNA polymerase III (Pol III) during replication.

18
Q

What do DNA polymerases always need to extend the DNA chain?

A

DNA polymerases always need a free 3’-OH group to extend the DNA chain.

19
Q

How is the free 3’-OH group provided for DNA chain extension?

A

The free 3’-OH group is provided by 10-60 nucleotides (primer) complementary to the template DNA chain.

20
Q

in what three types does DNA polymerases exist

A

Polymerase I
Polymerase II
Polymerase III

21
Q

Describe the coupling process by Pol I. Answer:

A

The coupling occurs through the nucleophilic attack of the growing DNA chain’s 3’-OH group and the phosphoryl of the incoming nucleoside triphosphate.

21
Q

what is the function of DNA polymerases I (POL I)

A

couples deoxynucleotides on DNA template.

22
Q

What is the result of the coupling process

A

This results in the elimination of pyrophosphate and its subsequent hydrolysis.

22
Q

Which other enzyme’s reaction does the overall process of Pol I resemble?

A

The overall reaction resembles that of RNA polymerase.

23
Q

What is strictly required by Pol I for the coupling process?

A

Pol I strictly requires that the incoming nucleosides be linked to the free 3’-OH group of the growing polynucleoside.

24
Q

What is the error rate of DNA Pol I?

A

The error rate of DNA Pol I is around one wrong base per 10 to 100 million.

25
Q

What enzyme catalyzes pyrophosphate hydrolysis?

A

Pyrophosphate hydrolysis is catalyzed by inorganic pyrophosphatase.

26
Q

How can Pol I work in reverse

A

Pol I can work in reverse by degrading DNA through pyrophosphorolysis.

27
Q

What is the specificity of Pol I based on?

A

Pol I is very specific; it recognizes the incoming dNTP according to the shape of the base pair it forms with the template and requires a Watson-Crick base pair with the template rather than direct recognition of the incoming base.

27
Q

What does it mean when Pol I is said to be processive

A

Pol I being processive means it can catalyze a series of successive polymerization steps (about 20 or more) without releasing the template.

Molecular Diagnostics (10 decks)

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