Nucleic acids structure and Mutations Flashcards
lecture 2
Mention the components of nucleic acid
- Phosphate groups
- Pentose sugar
- A nitrogenous base (purines including Adenine (A) and Guanine (G); and pyrimidines including Cytosine (C), Thiamine (T) and Uracil (U))
- RNA and DNA are two main nucleic acids
Define a nucleoside
A nucleoside a molecule is composed of a purine or pyrimidine base and a ribose or deoxyribose sugar
what is a nucleotide composed of
nucleotide is composed of nucleoside and phosphate group
5 functions of RNA
- Directs translation
- Ribosomal RNA have structural and enzymatic roles.
- Delivery of amino acids
- Participates in posttranscriptional processing
- Carrier of hereditary information in some viruses
Mention the 4 DNA stabilizing forces
- Sugar-phosphate chain conformation
- Base pairing using hydrogen bonds
- Base stacking and hydrophobic interactions
- Ionic interactions
What are the functions of DNA
- directs its own replication
- Direct the transcription of complementary RNA molecules
Define DNA mutation
The genotypic change as compared to the normal sequence
risk factors for DNA mutation
- Exposure to mutagenic agents like UV light, intercalating agents
- Errors in DNA replication and repair
Define polymorphism
Multiple forms of a gene or sequence variants with no obvious effect upon phenotype may be termed
under pont mutations, describe the other minor mtations under it
- Missense – results in a different amino acid
- Nonsense – results in stop codon hence termination of translation of the protein
- Silent - results in the same amino acid
- Transition - a purine replaced by a purine or a pyrimidine by a pyrimidine
- Transversion - a purine replaced by a pyrimidine or vice versa
Mention 2 types of mutations
- Point mutation
- Frameshift muatation
define frameshift mutation
The mutations that cause all of the subsequent three-letter codons to be changed
what does the cenral Dogma of biology states
The usual flow of genetic information is from DNA to mRNA to polypeptide
examples of frameshift mutation
- Deletions: involved loss of one or more nucleotides
- Insertion: involves the addition of one or more nucleotides into a gene
what are the two effects of mutations on proteins
- Loss-of-function: mutations can result in either reduced activity or complete loss of the gene product.
- Gain-of-function: mutations, result in either increased levels of gene expression or the development of a new function(s) of the gene product
Mention 6 enzymes that takes part in DNA replcation
- DNA topoisomerases
- Helicase
- RNA polymerase and primase
- Exonucleases
- Single strand binding proteins (SSBs)
- Ligases
what separates the two standed double helix of the DNA
DNA helicase
results of DNA replication
results in two daughter DNA duplexes that are identical to the original parent molecule
the synthesis of complementary strands occurs in which direction
5′ to 3′ direction
what directs DNA synthesis of a complementary DNA strand
DNA polymerases
where does replication occur
replication bubble
where does replication starts at
replication forks
differentiate the synthesis of leading strand and lagging strad
- The leading strand, is synthesized continuously.
- The lagging strand, is synthesized in Okazaki fragments
What direction does the DnaB protein translocate along the lagging strand template?
The DnaB protein translocates along the lagging strand template in the 5’ – 3’ direction.
function of DNA ligase
Its primary function is to join DNA strands together by forming phosphodiester bonds between nucleotide
Which direction do Rep helicase and PriA protein translocate along the DNA?
Rep helicase and PriA protein translocate along the DNA in the 3’ – 5’ direction.
What is the role of Single Strand Binding proteins (SSB) in relation to the separated strand of the dsDNA?
Single Strand Binding proteins (SSB) bind the separated strand of the dsDNA to prevent reannealing
What protective role do SSBs play regarding ssDNA?
SSBs protect the ssDNA from nucleases, which could degrade it.
How do SSBs prevent the formation of secondary structures in ssDNA?
SSBs prevent ssDNAs from forming fortuitous intramolecular secondary structures by binding to them and stabilizing the single-stranded DNA
How are SSBs removed from the ssDNA during DNA replication?
SSBs are stripped off the ssDNA by DNA polymerase III (Pol III) during replication.
What do DNA polymerases always need to extend the DNA chain?
DNA polymerases always need a free 3’-OH group to extend the DNA chain.
How is the free 3’-OH group provided for DNA chain extension?
The free 3’-OH group is provided by 10-60 nucleotides (primer) complementary to the template DNA chain.
in what three types does DNA polymerases exist
Polymerase I
Polymerase II
Polymerase III
Describe the coupling process by Pol I. Answer:
The coupling occurs through the nucleophilic attack of the growing DNA chain’s 3’-OH group and the phosphoryl of the incoming nucleoside triphosphate.
what is the function of DNA polymerases I (POL I)
couples deoxynucleotides on DNA template.
What is the result of the coupling process
This results in the elimination of pyrophosphate and its subsequent hydrolysis.
Which other enzyme’s reaction does the overall process of Pol I resemble?
The overall reaction resembles that of RNA polymerase.
What is strictly required by Pol I for the coupling process?
Pol I strictly requires that the incoming nucleosides be linked to the free 3’-OH group of the growing polynucleoside.
What is the error rate of DNA Pol I?
The error rate of DNA Pol I is around one wrong base per 10 to 100 million.
What enzyme catalyzes pyrophosphate hydrolysis?
Pyrophosphate hydrolysis is catalyzed by inorganic pyrophosphatase.
How can Pol I work in reverse
Pol I can work in reverse by degrading DNA through pyrophosphorolysis.
What is the specificity of Pol I based on?
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.
What does it mean when Pol I is said to be processive
Pol I being processive means it can catalyze a series of successive polymerization steps (about 20 or more) without releasing the template.
