General Flashcards
What does virulence mean?
The ability of a pathogen to cause disease. Its severity.
What Sugar is present in DNA nucleotides?
Deoxyribose sugar - is a pentose sugar.
Which carbon of the pentose sugar are nitrogenous bases attached to in a nucleotide?
1’
What carbon of the pentose sugar are phosphate groups attached to in a nucleotide?
5’
Which other nitrogenous base is bonded to Adenine and how many hydrogen bonds are present ?
Thymine
2
Which other nitrogenous base is bonded to Cytosine and how many hydrogen bonds are present ?
Guanine
3
How is DNA anti-parallel and what process is this helpful in?
One strand runs 3’ to 5’. The other runs 5’ to 3’.
Semi-conservative replication of DNA.
What are the 2 groove types in DNA?
Minor groove major groove.
How are the grooves within DNA helpful?
They allow stains such as SYBR green and Ethidium Bromide to fit into the grooves and stain DNA molecules. Useful in PCR and gel electrophoresis.
Name a dyes used in PCR/ gel electrophoresis.
SYBR green
Ethidium Bromide
What are enhancers in a DNA sequence? And what type of organisms are they most used in?
Enhancers are sequences that are linked with a promoter region and enhance the activity of the promoter region due to their associates with protein transcription factors. Enhancers mediate most selective gene expression in eukaryotes.
Which nitrogenous bases are purine?
Guanine and Adenine
Which nitrogenous bases are pyrimidine ?
Thymine and Cytosine
How many rings in a purine base?
2
How many rings in a pyrimidine base?
1
What is an intron?
A non-coding sequence of nucleotides which don’t code for an amino acid sequence or polypeptide chain.
What is an exon?
A coding region of nucleotides which code for a specific amino acid sequence.
When are introns present in mRNA?
Present in Pre-mRNA but not in mRNA.
How are introns removed from DNA?
Splices out by spliceosome enzyme.
What are intergenic regions of DNA and how are they useful?
They are non-coding sequences of DNA located between genes. These DNA sections are methylates to help maintain genomic integrity and prevent mutations.
What is illegitimate recombination?
2 unrelated DNA sections are joined.
Why are repetitive elements of DNA methylated?
To prevent neighbouring genes being transcribed when they are not supposed to by the presence of strong promoter regions. Helps maintain genomic integrity and prevent mutations. Prevents illegitimate recombination.
What are Pseudogones?
Former genes that have accumulated mutations that make them non-functional.
What is another name for Pseudogenes?
Vestigial genes
How are Pseudogenes often formed? (3 ways)
A gene whose protein is needed for survival.
When a gene is duplicated
Processed pseudogene.
What is a processed pseudogene?
Result of a DNA copy of mRNA being inserted into genome.
How is a pseudogene created when a gene is duplicated?
When a gene is duplicated one becomes a Pseudogenic gene and is non-functional and mutated. This doesn’t harm the organism because the other version of the gene remains functional and non-mutates.
Describe how DNA is packed to become a metaphase chromosome.
DNA helix wraps around histones to form nucleosomes (beads on a string). Loops of thick chromatin fibres from and are then further compacted into looped domains. The compact metaphase is then formed.
What makes the DNA pacing process highly specific?
Specific genes are always in the same place in the packed metaphase chromosome.
Why is heterochromatin hard to translate?
It is very densely and tightly packed so not many proteins are able to enter.
Why doesn’t heterochromatin contain much DNA?
Has long stretches of Satellite DNA.
Is euchromatin easy or hard to translate/transcribed and why?
Easy to transcribe because DNA is loosely packed around histones.
What is a solenoid?
6 nucleosomes joined together.
What is the area on a Solenoid where a lot of Adenine and Thymine are present?
Scaffold Attachment Area (SAR).
What is the scaffold attachment area on solenoids?
This is the sections of DNA where alot of Adenine and Thymine are present.
How is a super solenoid formed?
When SAR regions of multiple solenoids attach.
Who presented the structure of the DNA helix and in what year?
James Watson and Francis Crick.
1953
What method did Watson and Crick use to decide the structure of DNA?
Stick and ball methods.
What method did Maurice Wilkins use to decide the structure of DNA?
X-ray diffraction.
How does X-ray diffraction work when deciding the structure of DNA? (Brief).
X-rays shine onto and then bounce off the DNA molecule and create a complex pattern on photographic film. The film indicates the structure of DNA.
What allowed Watson to deduce that the sugar-phosphate backbone of DNA is smooth?
The bonding between A&T and G&C are exactly the same length. Therefore each rung of the DNA helix will be equal in length.
A famous experiment demonstrated that DNA could direct viral replication, providing evidence that DNA is the genetic material. Which scientists were directly involved in this experiment?
Alfred Hershey and Martha Chase
What is the purpose of Topoisomerases during DNA replication?
Work ahead of the replication fork to prevent supercoiling as the DNA opens.
What is Chargaffs ratio?
In a DNA sequence the ratio of A:T = C:G
Why is it impossible to have triple stranded DNA?
Some of the van Der Waals forces in DNA are too small/ weak to allow this.
Why can’t DNA have ribose sugar ? Why must it be de-oxyribose?
The extra oxygen atom would make the van Der Waals intermolecular forces become too close together and would change the physical structure of DNA.
When do neutrophils form?
During the initial stages of infection.
What cell type do Macrophages arise from?
Monocytes.
What are C3P and what is their purpose in immunity?
Recognise pathogens, attach to the surface of the pathogen and trigger an immune response. Compliment system with macrophages.
How is an MHC molecule formed?
Dendritic cells engulf the pathogenic antigens and present them on their surface to create a MHC molecule.
What happens when a MHC molecule has formed in the immune system ?
Cytotoxic T cells are activated and cause infected human cells to undergo autolysis and therefore kill the pathogen.
What are the 3 steps of DNA replication?
Initiation, Elongation, Termination.
Where does copying of DNA occur?
Replication fork
What is the purpose of DNA helicase in DNA replication?
Spins to unravel DNA helix whilst breaking hydrogen bonds between complimentary base pairs.
What is the leading strand of DNA?
The 3’ strand.
What is the lagging strand of DNA?
5’ strand - replicated with Okazaki fragments.
What direction does DNA helices work in?
5’ to 3’
When does DNA replication occur in Eukaryotes?
The S phase.
How was E.coli used to determine the semi-conservative nature of replicated DNA ?
Density gradient centrifugation was used. Before replication, only heavy nitrogen was present in the DNA. After 1 replication, there was an intermediate of both heavy and light nitrogen present. Couldn’t be conservative replication because no mixture of weighted nitrogen would be present. After the second replication , 75% of light nitrogen and 25% of heavy nitrogen was present - couldn’t be dispersive replication.
Describe the DNA that will be present after 1 and 2 replications in semi-conservative replication.
After 1 replication - 2 copies of DNA, both with one parent strand and one daughter stand.
After 2 replications - 2 copies with both parents strands, 2 copies with one parents and one daughter strand.
Name the overall features of DNA replication.
Semi conservative. Starts at the origin. Synthesis in the 5' to 3' direction. Unidirectional or bidirectional. Semi-discontinuous. RNA primers required.
Where does DNA replication start?
The origins
How many origin points for DNA replication do Eukaryotes have?
Many
What is the benefits of Eukaryotes having many origin points for DNA replication to begin?
Prevents replication stalling which can be harmful to a cell. Ensures that replication can happen rapidly. Acts as a backup incase some enzymes are unable to complete replication of one section of DNA.
Why can DNA synthesis only occur in the 5’ to 3’ direction?
DNA helices only works 5’ to 3’.
How does bidrectionality occur during DNA replication?
Replication forks move in opposite directions.
What are the benefits of bi-directional DNA replication?
Allows more than one section of DNA to be replicated at one time ad prevents replication stalling.
What is the REPLICON in DNA replication?
The region of DNA that is replicated from the start of the replication fork.
Are all origins of DNA Replication always active?
No - Only about 15% of origins are active at one time.
What is the benefit of only having some origins active at one time during DNA replication?
This allows time for proof reading and prevents mistakes in DNA replication.
What makes DNA replication semi-discontinuous ?
DNA polymerase works 5’ to 3’ so only the leading strand can be replicated continuously. The lagging strand is replicated discontinuously via Okazaki fragments.
Outline the process of DNA replication initiation.
- Pre-replication complex binds to origin.
- Accessor proteins bind to PRC.
- Components of the PRC are activated by Phosphorylation
- DNA polymerase are recruited
- Replication is initiated in the S phase
Why are accessory enzymes required in DNA replication initiation?
Allows enzymes such as DNA helicase and DNA polymerase to be able to bind to the parent strand.
What is the purpose of DNA gyrase in DNA replication?
Makes single strand nicks to relax supercooling. (Creates a cut in the double strand of DNA to help unwind the DNA and prevent the stress of un-winding), seals gaps in the sugar-phosphate backbone.
What is the purpose of RNA primase in DNA replication?
Catalyses he production of RNA primers?
What is the other name for RNA primase?
DNA polymerase alpha
What is the purpose of DNA polymerase during DNA replication?
Adds nucleotides in the 3’ to 5’ direction
What direction does DNA polymerase act in ?
5’ to 3’
What is the process of DNA replication in the leading strand?
Topoisomerases unwind the DNA helix and disrupt the sugar-phosphate backbones. DNA helices works 5’ to 3’ to break the hydrogen bonds between complimentary nucleotides. DNA primase adds RNA primers to the DNA. DNA polymerase adds complimentary nucleotides in the 3’ direction.
What are RNA primers produced by ?
Polymerase alpha
What is the purpose of DNA primase in DNA replication?
Adds RNA primers to the DNA.
Describe the process of DNA replication of the lagging strand.
Topoisomerase unwinds the DNA helix and disturbs the sugar-phosphate backbones. DNA helices breaks hydrogen bonds between complimentary base pairs. DNA primase adds many RNA primers to the lagging strand. DNA polymerase is then able too add nucleotides in the 3’ direction at each primer site. This creates Okaaki fragments. Polymerase delta uses RNA primers as an anchor to add bases to the lagging stand. RNAse H degrade RNA primers so that only DNA is left. A series of DNA with a gap in their backbone has been replicated. DNA ligase joins sugar-phosphate backbones.
What is the purpose of RNAse H in DNA replication?
Degrades RNA primers so that only DNA is present in the final replicated DNA.
What is the purpose of DNA ligase in DNA replication?
Join the sugar-phosphate backbones in the lagging strand.
What triggers the termination phase of DNA replication?
The collision of two replicative forks between two active replication origins.
What are the reasons why DNA replication may enter the termination phase?
Chromosome ends, replication issues, can’t fit another primer, lose chromosomal DNA.
What is the purpose of the telomere?
Protective cap at the end of the DNA strand. Prevents chromosome fusion by non-homologous ends joining.
What molecules is Telomerase made of ?
hTERT - human telomerase reverse transcriptase.
hTP - telomerase RNA
What type of template (DNA or RNA) does telomerase use?
RNA
What is the purpose of the telomerase enzyme in DNA replication?
Extends the telomere - adds repeating sequences of nucleotides to the 3’ end of the DNA strand.
What happens when the telomere shrinks and becomes very small?
Cellular senescence
What is cellular Senescence ?
Once the telomere shrinks to a certain extent, the cell stops dividing as he telomere is lost. Cell morphology changes and gene mutations may occur.
What are cell morphology changes?
Breakdown of the cell wall, disfunction of organelles, cells become unattached from each other etc.
Which strand in mitochondrial DNA is used for replication?
The H strand in mammalian mitochondrial DNA.
What happens to the original L strand of mitochondrial DNA during mitochondria DNA replication?
Remains single stranded and un-replicated.
Which side of a DNA strand add nucleotides to ?
3’ end
Where is DNA polymerase Gamma present and what is its purpose?
In the mitochondria . Used to Replicate mitochondrial DNA .
Where are all DNA Polymerases (except DNA polymerase gamma) located?
Nucleus
Where is DNA polymerase beta present and what is its function?
Nucleus of non-dividing cells. Helps aid DNA repair .
Where do DNA polymerases add new nucleotides to on the strand ?
3’ end hydroxyl group .
How does DNA polymerase I act as a exonuclease in DNA replication?
Removed ribonucleotides in the from the 5’ end of Okazaki fragments allowing them to be replaced with deoxyribonucletoides so that fragments consist of DNA only .
What shape is an E.Coli chromosome?
Circular
How is telomerase able to be complimentary and act on the telomere?
It carries its own template RNA which is complimentary to the telomere repeat sequences .
What happens to the overhanging 3’ end of the chromosomes in eukaryotes at the end of DNA replication?
They form loops .
Which strand of DNA is the coding strand?
The lagging strand
Which strand of DNA is the non-coding strand?
The leading strand
How many types of RNA polymerase exist in eukaryotes?
3
How many types of RNA polymerase exist in bacteria?
1
What is the purpose of enhancer sequences in DNA replication and how do they work?
Bind to activator proteins and alter the 3D structure of DNA to help attract DNA Polymerase II and therefore regulate transcription .
What proteins facilitate looping of the DNA during DNA replication and which proteins does looping allow to interact?
Activator proteins - Allow proteins bound to the enhancer and proteins bounds to the promoter to interact .
What proteins prevent the looping of DNA?
Repressor proteins .
Are terminator genes located upstream or downstream from the coding region?
Downstream
Write an overall definition for eukaryotic transcription.
The use of DNA as a template to produce mRNA.
Why is DNA changed into mRNA before entering the cytoplasm?
The cytoplasm would be too hostile and degrade the DNA.
Where does eukaryotic transcription occur?
The nucleus
What is the difference I the sugar present in DNA and RNA?
RNA has Ribose but DNA has 2’- Deoxyribose.
What is the different base in RNA compared with DNA?
Thymine in DNA, Uracil in RNA.
What is the structural different between uracil and thymine?
Uracil has one less methyl group than Thymine.
What is the advantage of Thymine having the extra methyl group compared to Uracil?
The methylation makes the DNA more protected and restricts Thymine to only binding with Adenine.
What is the general function of mRNA?
Codes for proteins
What is the general function of rRNA?
Form the basic structure of the ribosome and catalyse protein synthesis.
What is the general function of tRNA?
Used in protein synthesis as an adaptor between mRNA and amino acids.
What are the benefits of having mRNA as an intermediate between RNA and DNA?
Controls the location and transcription of DNA. Allows amplification. mRNA is less likely to be degraded in the cytoplasm than DNA.
How does having mRNA as an intermediate allow amplification of transcription?
In DNA we only have one copy of a gene so transcription would be very slow. Whereas using mRNA means many copies of the gene can be present and therefore allow alot of transcription of the gene to occur at once.
What is required for RNA polymerase to bind to DNA?
Transcription factors.
What are transcription factors?
Proteins that bind in or near the promoter regions of the gene or at regulatory gene sequences to control gene expression.
What are the optional sequence elements that transcriptional factors bind to?
Basal promoter elements - in or near promoter regions.
Proximal promoter elements - sequences that are further away from the promoter region.
What are cis-acting transcriptional factor elements?
Sequence elements present on the same DNA molecules as he gene they affect.
What are trans-acting transcriptional factors?
Sequence elements that interact with genes on any DNA molecule or gene within the cell. They are able to move throughout the cell.
Where is RNA Polymerase I found and what is it overall purpose?
Nucleolus
Transcribes rRNA
Where is RNA Polymerase II found and what is its overall purpose?
Nucleus
Transcribes mRNA and genes for some species of small RNA.
Where is RNA III found and what is its overall purpose?
Transcribes tRNA and 5S rRNA genes.
Describe the complex of RNA polymerase II.
It is a hollow enzyme complex made up of many different accessory proteins such as RNA Polymerase II enzyme, a subset of general transcription factors and many regulatory proteins.
What is the transcription initiation complex and what is its purpose?
TATA box is surrounded by a selection of different transcription factors.
Allows the un-zipping of DNA for replication to occur.
Describe the elongation process of DNA transcription.
The dimer protein ‘FACT’ binds to nucleosomes immediately ahead of the transcribing RNA polymerase II. This partly dissembles the nucleosome (removes 2 of the 8 histones) so that RNA Polymerase II can transcribe the DNA wrapped around the nucleosome. ‘FACT’ the reassembles the nucleosome being RNA Polymerase II by returning the missing histones.
Exactly how does the dimer protein ‘FACT’ disrupt the nucleosome during DNA transcription?
Removes 2 of the 8 histones.
What are the 3 stages of DNA transcription?
Transcription initiation complex, elongation, termination.
Describe the allosteric model of DNA transcription termination.
At a termination polyadenylation signal, the binding of the RNA Polymerase II and its accessory proteins is disabled. Polymerase II can no longer bind to the DNA and transcribe it.
What are the 2 models for DNA transcription termination?
Allosteric model and Torpedo model.
Describe the torpedo model for the termination of DNA transcription.
RNA polymerase II produces mRNA to be longer than the gene. mRNA is cut and detached from RNA Polymerase II at the cleavage site.
Xrn2 can bind to the end of the remaining mRNA which is still attached to RNA polymerase II and degrade the remaining DNA towards the enzyme. When Xrn2 collides with RNA Polymerase II, RNA polymerase is knocked off the DNA strand terminated transcription.
How is Pre-mRNA processed to form mRNA ?
A cap is added to the 5’ and a Poly A tail is added to the 3’.
Splicing introns using a spliceomere.