Genomes Flashcards
What is gel electrophoresis? (2 points).
- Used to separate DNA fragments based on their size so they can be identified and analysed.
- It is based on the fact that the rate at which a particular fragment of DNA moves is proportional to its mass.
Describe the process of gel electrophoresis (3 points).
- DNA is hydrolysed by restriction enzymes before it can be separated. The hydrolysed DNA sample is placed within the well at one end of the agarose gel. The gel is placed in a buffer so that the negative electrode is next to the well and an electrical current is passed through the gel.
- As DNA is negtively charged (due to the phophate group), DNA fragments migrate toward the positively charged end of the gel / electrode.
- Smaller DNA fragments migrate through the gel more quickly than larger fragements. So smaller fragments move further along the gel in the same period, this process separates fragments according to their size across the gel.
Describe how the DNA fragments are visualised using Southern blotting and autoradiography (4 points).
- An alkali is added to make the DNA single-stranded.
- The DNA is transferred to a nylon membrane by Southern blotting.
- Radioactively / fluorescently labelled DNA probes with complementary base sequences to the DNA and bind due to hydrogen bonding.
- The DNA can be visualised using autoradiography (the radioactively labelled probes expose X-ray film so bands can be visualised).
Describe DNA sequencing (16 points).
- DNA is broken into fragments 200-600 base pairs long.
- Adenine A-base is added to 3 prime ends of each fragment.
- Adapters (short sequences of DNA) are attached to each end of the fragments.
- Double strands of DNA are then separated into single strands.
- These are washed across a flow cell (small plastic slide with primers- lots of small peices of DNA attached).
- DNA bind to complementary primers.
- Excess DNA is washed away.
- DNA polymerase and bases are added.
- A complementary strand of DNA is made.
- The attached DNA fragment is used to make lots of copies via bridge amplification.
- Complementary strand bends and is made along the bridge.
- DNA is denatured.
- Primers, DNA polymerase and fluorescently labelled DNA bases are added.
- DNA polymerase adds fluorescent base.
- Coloured lasers causes colours to grow.
- Camera detects.
Definition of proteome.
All the proteins produced in a given type of cell or organism at a given time.
Definition of PCR.
To amplify fragments of DNA in an automated process.
Definition of in vitro.
Experiment / processes carried outside living cells in test tubes.
Definition of primers.
Short sequence of nucleotides that have a complementary base sequence to one end of the DNA strand to be copied. They allow the DNA polymerase to attach and start addition of nucleotides. They prevent strand re-joining.
Describe polymerase chain reaction method (PCR)- an in vitro method of cloning (5 points).
- Separation of DNA strand: the mixture is heated to 95 degrees which breaks the hydrogen bonds between bases, therefore separates the strands and produces single-stranded DNA molecules. DNA has become denatured.
- Addition of the primers: the temperature is reduced to 55-60 degrees to allow primers to bind to the ends of the single-stranded DNA molecules- annealing.
- Synthesis of DNA: the temperature is increased to 72 degrees. This enables the free DNA nucleotides to attach by complementary base pairing. The new DNA strands are built up using the enzyme tag polymerase which joins the phosphodiester bonds- extension. The first cycle is complete.
- The cycle is repeated.
- The 2 resulting DNA molecules make up the template DNA fro the next cycle, thus amplifying the amount of DNA duplicated for each new cycle.
List the pros of in vivo cloning (7 points).
- Very useful when introducing a gene into another organism, therefore can be used in gene therapy.
- Uses vectors and plasmids which means the gene can be delivered into the other organism.
- Produces transformed bacteria which can be used to produce large quantities of gene products, for example: insulin.
- Almost no risk of contamination due to the use of restriction endonucleases and creation of sticky ends.
- Very accurate, the copied DNA has very few errors as mutations are rare.
- It can be used to copy genes which have not been studied before.
- Reliably copies genes up to about 2 million base pairs long.
List the cons of in vivo cloning (2 points).
- It takes a long time to produce enough DNA.
- Cannot be copiedunless isolated from other material.
Pros of in vitro cloning (4 points).
- Extremely rapid.
- No valuable time is lost before forensic analysis and matchng can take place.
- Does not require living cells, it can copy DNA which has been partly broken down
- DNA embedded in other material can be copied.
List the cons of in vitro cloning (5 points).
- Any contaminating DNA found at a crime scene will massively be increased.
- Requires a very pure sample to prevent contaminant DNA being multiplied.
- An errors in copying DNA will also be copied in subsequent cycles.
- It cannot be used to copy genes which have not been studeied before.
- Unrelaible when copying fragments longer than 1000 base pairs long.
Describe generally how to produce genetic fingerprints (8 points).
- Extract the DNA: Crime scene / individual / cells and tissue.
- Amplify the DNA: PCR.
- Digestion of DNA: Restriction endonucleases.
- Seaparation: Gel electrophoresis.
- Southern blotting: Transfer to nylon sheet.
- Hybridisation: Add radioactive / fluorescently labelled probes.
- Development: Place nylon layer under UV light or expose to X-ray.
- Interpreation: Make comparisons between bonds / locate specific genes using a DNA ladder.
Describe how the technique for genetic fingerprinting is carried out. Markscheme 1 (10 points).
- DNA is cut.
- Using restriction enzymes.
- Electrophoresis.
- Separates according to length / mass / size.
- DNA is made single-stranded.
- Transfer to membrane / Southern blotting.
- Apply probe.
- Radioactive / single-stranded / detected on film / fluorescent.
- Reference to tandem repeats / VNTR’s / minisatellites.
- Pattern unique to every individual.