DNA and Genomics Flashcards
Describe the 3 hypotheses of DNA replication, focusing particularly on
the semi-conservative model.
1) Semi-conservative replication
- both strands separate by the breaking of hydrogen bonds and each strand acts as a
template for the synthesis of a new strand through complementary base pairing. Thus each DNA molecule formed is a hybrid consisting of 1 original strand and 1 newly synthesized strand.
2) Conservative replication
-2 parental strands re-associate after acting as templates, thus restoring the original double helix. The other DNA molecule consists of 2 newly synthesized strands.
3) Dispersive replication
Parental DNA molecule is fragmented and dispersed. Daughter molecules are made up of a
mixture of old and newly synthesized parts
Describe the structural features and the properties of DNA that make
it suitable as a store of information.
It is a suitable store of information as:
a) It can be replicated accurately -> daughter cells have identical copies of DNA as the parent cell.
Weak hydrogen bonding between the two strands allow them to separate and act as a template for new strand synthesis
b) It is a stable molecule -> can be passed on to the next generation without loss of the coded information
Collectively, numerous hydrogen bonds hold the two strands of DNA together and adjacent nucleotides in each strand are joined by strong covalent phosphodiester bonds
c ) There is a backup of code
DNA is double stranded and one strand to serve as a template for the repair of the other if a mutation occurs on either one
d) Coded information can be readily utilised/accessed
Weak hydrogen bonding allows the template strand to separate from the non-template strand allowing transcription to take place
Complementary base pairing allows the faithful transfer of info from DNA to RNA in transcription, which will be translated to protein subsequently
Describe DNA replication: unzipping of parental strand.
- Replication begins at specific points of the DNA molecule
each of which is known as an origin of replication (ori). - Helicase binds to orgin of replication. It disrupts hydrogen bonds between complementary base pairs, causing parental strands to unzip and separate. This process requires ATP.
- Single-strand binding proteins keep the strands apart so that they can serve as templates for the synthesis of new strands.
- Topoisomerase relieves “overwinding” strain ahead of replication forks by breaking, swiveling and rejoining DNA strands.
Describe DNA replication: addition of primer.
- RNA primer is added to each template (parental strand) by the enzyme primase.
- RNA primer provides a free 3’ OH end for DNA polymerase to recognise and start DNA synthesis of the complementary daughter strand.
- DNA polymerase can only add deoxyribonucleotides (DNA nucleotides) to a pre-existing 3’ OH end of a nucleotide.
Describe DNA replication: synthesis of daughter strands.
- DNA polymerase uses the parental strand as a template and aligns the free activated deoxyribonucleoside triphosphates (dNTPs) in a sequence complementary to that of the parental strand.
- DNA polymerase catalyses the formation of phophodiester bonds between adjacent daughter DNA nucleotides of the newly synthesised strand.
- As DNA polymerase moves along the template, it proof reads the previous region for proper base pairing. Any incorrect deoxyribonucleotide is removed and replaced by a correct one.
- The leading strand is synthesised continuously in the 5’ to 3’ direction.
- The lagging strand is synthesised discontinuously. It is synthesised in fragments known as Okazaki fragments. Each fragment is initiated by an RNA primer before the addition of DNA nucleotides.
- A different DNA polymerase then removes the RNA primer and replaces it with deoxyribonucleotides.
- DNA ligase seals the nicks by forming phophodiester bonds between adjacent nucleotides of each of the DNA fragments of the new strand.
Describe DNA replication: end of replication.
- Complementary parental and daughter strands rewind into a double helix.
- Each resultant helix consists of one parental strand and one daughter strand. Hence, called semi-conservative replication.
Describe the end replication problem.
During DNA replication, DNA polymerase needs a free 3’ OH group to add free nucleotides to the growing DNA strand.
For one of the daughter chromosomes, this limitation leads to a 3’ overhang because the 5’ end of its newly-synthesised daughter strand will have the RNA primer removed without replacement with DNA, because no 3’ end available for DNA polymerase.
Describe how the presence of telomeres prevents the harmful effects of the end replication problem.
-Telomeres are nucleotide sequences found at both ends of eukaryotic chromosomes.
-They are non-coding regions of DNA made up of a series of tandem repeat sequences.
-Since telomeres are non-coding, the shortening of the chromosome ends (i.e. telomeres) first, do not result in much deleterious effects. The genes within the chromosome are thus protected.
Describe the central dogma.
The central dogma is the flow of genetic information from DNA to RNA through transcription, RNA to protein through translation of nucleotide sequences on RNA to an amino acid sequence in protein.
Explain why the genetic code is a triplet code.
If 3 nucleotides code for 1 amino acid:
-protein can contain up to 4^3 = 64 amino acids, more than sufficient to code for 20 amino acids
-these 64 codons form the set of instructions that tell a cell the order in which AA are to be joined to form protein
Describe RNA transcription: initiation
(a) General transcription factors first assemble along the promoter.
(b) General transcription factors recruit RNA polymerase and position it correctly on the promoter
(c) The complex of RNA polymerase and transcription factors is called the transcription initiation complex.
- RNA polymerase attach to the promoter with the aid of portein factors.
- RNA polymerase unzips and separates the DNA double helix at the promoter by breaking hydrogen bonds between complementary base pairs.
- Only one strand is used as the template to synthesise complementary strand.
Describe RNA transcription: elongation
- Free ribonucleotides will bind by complementary base pairing to deoxyribonucleotides on DNA template strand.
- Cytosine, guanine, adenine, and uracil containing ribonucleotides will complementary base pair with guanine, cytosine, thymine and adenine containing deoxribonucleotides on the DNA template respectively
- Cytosine forms 3 hydrogen bonds with guanine, adenine form 2 hydrogen bonds with thymine and uracil.
- RNA polymerase catalyses the formation of covalent phosphodiester bonds between adjacent ribonucleotides, forming the sugar-phosphate backbone of the growing mRNA transcript.
- mRNA strand is synthesized in the 5’ to 3’ direction as new ribonucleotides are added to the 3’ OH end of the growing mRNA strand
- As the transcription complex continues to move down the DNA double helix, unzipping the 2 strands, and synthesizing mRNA, the region of DNA that has just been transcribed, reanneals.
Describe transcription: termination.
- After RNA polymerase transcribes through the termination sequence, the mRNA chain is released and the RNA polymerase will dissociate, terminating transcription.
(a) RNA polymerase transcribes a sequence on the DNA, which codes for a polyadenylation signal (AAUAAA) in the pre-mRNA,
Describe post-transcriptional modification and explain its significance.
- Addition of 7-methylguanosine cap to 5’ end of pre-mRNA
- protects mRNA from degradation by ribonucleases, facilitates the export of mature mRNA from the nucleus to the cytoplasm & helps the cell recognize mRNA (amongst all other RNAs in cell) so that it can undergo subsequent steps such as splicing - RNA splicing involves spliceosomes which excise introns & join exons.
- Synthesis of poly A tail (polyadenylation) involves the cleaving of the pre-mRNA by an endonuclease 10-35 nucleotides downstream of the polyadenylation signal and the addition of many adenine nucleotides by the enzyme poly A polymerase downstream of the polyadenylation signal, AAUAAA.
-> protects mRNA from degradation by ribonucleases, facilitates the export of mature mRNA from the nucleus to the cytoplasm and interacts with initiation factors (together with 5’cap) to form the translation initiation complex.
Describe the process and explain the significance of amino acid activation
-Firstly, each specific amino acid is covalently bonded to its specific tRNA, with a specific anticodon, at its 3’ stem, forming an amino-acyl tRNA.
-Catalysed by aminoacyl-tRNA synthetases.
-an aminoacyl-tRNA synthetase has specific active sites that are complementary to conformation and charge of
1. specific amino acid
2. specific tRNA with specific anticodon
tRNA activated with correct amino acid as:
-each enzyme has specific active sites that are complementary in 3D conformation and conform to :
1. the different tRNAs through unique identity sites at acceptor stem and/or anticodon loop of specific tRNA molecule
2. and specific amino acid
