DNA Flashcards
What gene mutation is associated with xeroderma pigmentosa? How does this mutation lead to the associated disorder?
A mutation in the NER gene - this gene codes for an enzyme which is used nucleotide excision repair - a dysfunctional gene here won’t recognise and replace abnormal DNA - UV induced DNA damage is not adequately repaired, so a prolonged exposure to ultraviolet light leads to a greater propensity to developing skin cancer
Describe 2 ways in which chemotherapy may actually be more harmful to a cancer patient.
Chemotherapy-induced damage - where the chemotherapy itself may be causing DNA damage that is beneficial to the growth and survival of the cancer cell germ line
Differential sensitivity -
Describe how DNA helicase functions.
DNA helicase breaks the hydrogen bonds that hold the alpha helical DNA molecule in its secondary structure, unraveling the DNA
What is the end-replication problem? How is this resolved?
The end-replication problem relates to the fact that no primer can be put at the end of a bit of DNA to copy the full sequence - therefore every time DNA will be lost - DNA telomerase resolves this by adding G & C repeats onto the end of DNA fragments in order to extend it, allowing primers to bind to copy the remaining bit of coding DNA
How may chemotherapy actually be detrimental to the patient?
The chemicals involved in chemotherapy itself may actually induce harmful mutations to a patients DNA
Why after continued chemotherapy treatment may a cancer begin to proliferate again?
The chemotherapy may be acting only one a specific cell within the cancer, whereas cells within the cancer itself may have mutated and formed various phenotypes which may be resistant to chemotherapy
How may inhibitors of DNA synthesis be used as antibiotics?
They may inhibit the enzymes responsible for the synthesis of DNA
What is non-homologous end joining? What is a potential problem with this repair mechanism?
Non-homologous end-joining involves the joining of the DNA flanking gap in a double stranded DNA break - this however will lead to deletion of the sequence which has been lost from the original DNA strand
What is an inversion?
A reversal of the order of a sequence of genes in a chromosome from their original/normal order
What is a translocation?
A translocation is the interchanging of genetic sequences between 2 non-homologous chromosomes
List 2 types of inversion. How do they differ?
Pericentric inversion - an inversion that involves reversing the order of a genetic sequence that includes the centromere
Paracentric inversion - an inversion that reverses the order of a genetic sequence that does not include the centromere
What is an inversion?
A reversal of the order of a sequence of genes in a chromosome from their original/normal order
What is a translocation?
A translocation is the interchanging of genetic sequences between 2 non-homologous chromosomes
List 2 types of inversion. How do they differ?
Pericentric inversion - an inversion that involves reversing the order of a genetic sequence that includes the centromere
Paracentric inversion - an inversion that reverses the order of a genetic sequence that does not include the centromere
How many bases are their every turn of the DNA double helix?
10
What is a TATA box?
A sequence of nucleotides within a promoter region specifying where transcription will begin
How far upstream from the actual transcription site is the TATA box located?
Around -10 base pairs upstream
Within a TATA box what is the sequence of bases?
TATAAA
What is the difference between pre-mRNA and mature mRNA?
Mature RNA exists after certain modes of protection have been added to pre-mRNA
List 3 ways in which pre-mRNA is transformed to mature mRNA.
- 5’ cap
- addition of a polyA tail
- splicing
What are the non-coding parts of DNA called? What are the coding parts called?
Non-coding parts are called introns - the coding parts are called exons
At which ends of the pre-mRNA does capping and polyadenylation occur? What is the supposed mechanism of these processes?
Capping occurs at the 5’ end (producing a 5’ cap) and polyadenylation occurs at the 3’ end (producing a 3’ polyA tail) - these processes both act to protect the mRNA from degradation
What is splicing?
Splicing is the removal of non-coding sections of DNA from the mRNA sequence
Describe briefly the structure of the 5’ cap.
A guanosine is methylated on the 7 position
Briefly describe the process of polyadenylation.
Endonuclease activity initially cleaves the mRNA molecule at a specific site, where polyA polymerase acts to add as many as 200 adenine bases
How many adenine bases may be in an mRNA polyA tail?
As many as 200
What is a polysome/polyribosome?
A collection of ribosomes held together by a strand of mRNA which they’re all helping to translate
What, and how many, molecules make up the basic structure of a eukaryotic ribosome? What 2 subunits do they compose?
4 rRNA’s and 82 proteins - these make up the 40s and 60s subunits
What, and how many, molecules make up the basic structure of a prokaryotic ribosome? What 2 subunits do they compose?
3 rRNA’s and 56 proteins - these make up the 30s and 50s subunits
What are the seperate names for the prokaryotic and eukaryotic ribosomes?
The prokaryotic ribosome is called the 70s ribosome, while the eukaryotic ribosome is called the 80s ribosome
Which triplet in the DNA code is used to initiate translation? What amino acid does this code?
AUG - this codes for a methionine
Describe specifically what makes up each subunit in the 80s ribosome? Is this ribosome eukaryotic or prokaryotic?
The 80s ribosome is eukaryotic and is composed of:
- a 60s subunit which is composed of:
- 5s RNA, 5.8s RNA, 28s RNA, and 49 proteins
- a 40s subunit which is composed of:
- 18s RNA and 33 proteins
Which nucleotide triplets code for a stop codon? What amino acids do these code for?
UAA, UAG, & UGA - these triplets don’t actually code for any amino acid
In tRNA structures, how are the stem loops held in conformation?
The anti-parallel sequences that make up the stem loop are held together by hydrogen bonds
How does tRNA interact with mRNA?
The anti-codon of a tRNA is complementary to a codon (a sequence of 3 RNA nucleotides) and so will bind it - the tRNA carries a specific amino acid which is coded for by the codon sequence, and tRNA binding via the anti-codon ensures that this amino acid will be incorporated into the protein being translated in order
What is the wobble hypothesis?
This concept states that the 3rd nucleotide of a codon may bind to the 1st nucleotide in the anti-codon using non-Watson-Crick base-pairing
What is an anticodon?
A complemtary 3 base code on the tRNA to the codon on an mRNA
Which enzyme catalyses the transfer of an amino acid onto a tRNA molecule? Where is this attachment site?
Aminoacetyl-tRNA synthetase - they are attached to the 3’ end of the tRNA
What are the P-site and A-site in a ribosome?
The A site (aminoacyl) is the first binding site of a tRNA molecule, and the p site (peptidyl) is the second binding site of a tRNA molecule
What initiates termination of translation?
A stop codon, which is recognised by a release factor, which binds and results in the release of the polypeptide chain created by the ribosome
What triplet code gives rise to a start codon? What amino acid does this code for?
AUG - this codes for a methionine
A DNA sequence is often decried as comma-less, what does this mean?
There are no gaps in the reading frame of the DNA sequence
How many nucleotides code for a single amino acid? What is this called?
3 - this is called the triplet code
Why are there so few rRNA’s, and so many mRNA’s?
Ribosomes show relatively little variation, so the rRNA that comprises them also shows little variation across different times - mRNA code proteins that show an extraordinary amount of variation, and so encompass a huge volume
Why do DNA polymerases shave a greater proof-reading capacity than RNA polymerases?
Abnormal DNA would produce universally abnormal proteins downstream which could potentially affect the viability of the cell and the organism - they will also be passed onto daughter cells - therefore DNA changes hold a greater priority in terms of having to be corrected - abnormal RNA will only affect a few proteins downstream, won’t affect any daughter cells, and so is no as great a priority to correct as the universal changes cause by abnormal DNA
How many RNA polymerase do prokaryotes have in comparison to eukaryotes?
Prokaryotes have just 1, whereas eukaryotes have 3
Does the anticodon of tRNA bind to the A site or P site of a ribosome?
It binds to the A site
What occurs at the P site?
Covalent bonds (peptide) are formed between the existing amino acid polypeptide and the amino acid attached to the tRNA occupying the A site
What performs splicing?
The spliceosome
What is thought to control splicing? How may mutations here affect splicing?
Specific sequences in introns promote splicing - mutations here may mean they are not recognised as introns and as such not spliced
In which area of the cell does transcription occur? In which compartment does translation occur?
Transcription occurs in the nucleus - translation occurs in the cytoplasm
State how the antibiotics tetracyclin, chloramphenicol, and erythromycin affect the ribosome.
- tetracyclin - binds the 30s subunit - prevents aminoacyl tRNA binding - the A site therefore cannot be occupied
- chloramphenicol - binds the 50s subunit - affects peptidyl transferase action - peptide bonds can’t form between amino acids
- erythromycin - binds the 50s subunit - affects translocation from the A site to the P site - the A site therefore remains occupied
What base pair is formed using 3 hydrogen bonds?
Cytosine & guanine
What base pair is formed using 2 hydrogen bonds?
Adenine & thymine
What nuclear bases are purines?
Adenine & guanine
What nuclear bases are pyrimidines?
Thymine & cytosine
DNA is often described as having a ‘twisted-rope ladder’ structure. What molecules would form the steps and ropes of the ladder?
- the nitrogenous bases would make up the steps
- the phosphodiester bonds that join the 5’ -phosphate group and the 3’ -hydroxyl group
Where do most DNA-binding proteins bind the DNA alpha helix? Why?
At the major groove - it has a greater area for DNA to bind
Does euchromatin stain dark or light?
Light
Does heterochromatin stain dark or light?
Dark
What is the genome?
The complete set of information an organism carries in its genes
How is a nucleosome composed?
It is composed a a histone octamer (8 histones) which the DNA strand is wrapped around
What does the ‘beads on a string’ describe?
The histone octamers that form the nucleosome, and the DNA wrapped round it, with linker DNA joining adjacent histone octamers
What keeps the DNA wrapped round a histone octamer?
Histones contain various positive amino acid residues in their structure, such as lysine and arginine, which attracts the negatively charged DNA sequence - hydrogen bonds are also formed between the 2 structures
Is euchromatin or heterochromatin highly condensed?
Heterochromatin is highly condensed
What is the short arm of a chromosome called? What is the long arm called?
A chromosomes short arm is called the p arm - a chromosomes long arm is called the q arm
What determines whether a nucleic acid is a nucleotide or a nucleoside? What then is the difference between the 2?
Whether the nucleic acid has an attached phosphate group - a nucleotide contains this phosphate group, while a nucleoside doesn’t
What is a nucleic acid with an attached phosphate group called?
A nucleotide
What 3 structures comprise a nucleotide? What bond joins them together?
A nuclear base, sugar (pentode sugar), and a phosphate group - these are all joined by covalent bonds
What pentode sugar is found in DNA? What pentode sugar is found in RNA
2-deoxyribose is found in DNA - ribose is found in RNA
Draw the structure of 2-deoxyribose. How does this differ to the structure of a ribose sugar?
~have to check structure drawing for yourself~
What charge does a phosphate group on a nucleotide?
A negative charge
Is DNA hydrophobic or hydrophilic? Why is this?
DNA is hydrophilic (it attracts water) as it has an overall negative charge, as a result of the attached phosphate group
What type of bond are the nucleotides in a linear sequence joined by?
A phosphodiester bond
Draw the structures of adenine, guanine, cytosine, and thymine.
~check slides~
Name the 4 nucleosides and corresponding nucleotides found in RNA.
- guanosine - guanosine monophosphate
- adenosine - adenosine monophosphate
- cytidine - cytidine monophosphate
- uridine - uridine monophosphate
Name the 4 nucleosides and corresponding nucleotides found in DNA.
- deoxyadenosine - deoxyadenosine monophosphate
- deoxyguanosine - deoxyguanosine monophosphate
- deoxycytidine - deoxycytidine monophosphate
- deoxythymidine - deoxythymidine monophosphate
What nuclear base replaces thymine in RNA?
Uracil
What links the nuclear bases on opposing strands?
Hydrogen bonds
What base does adenine bind in RNA? How many hydrogen bonds link the 2 nuclear bases?
Uracil - they are linked by 2 hydrogen bonds
DNA strands in a double helix are said to be anti-parallel. What does this mean?
The opposite strands run in a way where the polarity of one strand is orientated in the opposite direction to the other
How is a single nucleotide universally read?
5’ to 3’ left to right
What happens to the strand of DNA that is copied for DNA synthesis?
A strand from this sequence will go into 1 daughter strand each
How are Okazaki fragments sealed together?
By DNA ligase
In the classical X-shaped chromosome after replication, what is the number of chromosomes, chromatids, and DNA molecules?
- 1 chromosome
- 2 chromatids
- 2 DNA molecules
What is the function of DNA helicase?
DNA helicase breaks the hydrogen bonds joining the 2 DNA sequences, unraveling the DNA alpha helix
What structures are formed by DNA polymerase on the lagging strand in DNA replication?
Okazaki fragments
How is DNA replication elongated in the plasmids of prokaryotes?
Via 2 replication forks
What is chromatin?
Chromatin is the combination of protein and DNA
Why are nucleoside analogues often used in antiviral drugs as opposed to nucleotides analogues?
Nucleoside analogues are missing the 5’ phosphate group - therefore they cannot be incorporated into the DNA of invading pathogens, and they will not be able to multiply and replicate
What is the difference between an exonuclease and an endonuclease?
Exonucleases cleave external phosphodiester bonds at the end of a nucleotide sequence - endonucleases cleave internal phosphodiester chains within the nucleotide sequence
What type of restriction activity is present in DNA polymerase? What is its role?
DNA polymerase contains innate endonuclease activity - this acts as a proof-reading merchants and can correct any incorrect base pairing at the 3’ OH- end
What is the function of topoisomerase?
Topoisomerase prevents DNA from overwinding during replication, by introducing single-strand breaks (these are resealed after completion of transcription)
What is the role of DNA primase?
This adds an RNA primer for DNA polymerase to instigate DNA synthesis
What is a transition?
A substitution mutation involving the exchange of a purine for another purine or a pyrimidine for a pyrimidine
What is a transversion?
Asubstitution mutation involving the exchange of a purine for a pyrimidine or a pyrimidine for a purine
What are the terms ‘A site’ and ‘P site’ abbreviations of?
- A site = aminoacyl site
- p site = peptidyl site
