MedSensor Flashcards
WHAT IS DNA? - composition, features, function
DNA is made of two linked strands a double helix. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four bases: adenine (A), cytosine (C), guanine (G) or thymine (T). DNA bases pair up with each other, A with T and C with G, to form units called base pairs. It contains all the genetic information needed for an organism to develop, survive and reproduce.
How does DNA-origami work & what can it be used for?
Nanoscale folding of DNA to create 2D/3D shapes at the nanoscale. The specificity of the complementary base pairs is used. Is used for the construction of nanorobots and other structures
How does PCR work and what does it do?
- Denaturation (@94-96°C)
This step is the first regular cycling event and consists of heating the reaction
chamber to 94–98 °C (201–208 °F) for 20–30 seconds. This causes DNA
melting, or denaturation, of the double-stranded DNA template by breaking the
hydrogen bonds between complementary bases, yielding two single-stranded
DNA molecules. - Annealing (@68°C)
In the next step, the reaction temperature is lowered to 50–65 °C (122–149 °F)
for 20–40 seconds, allowing annealing of the primers to each of the single-
stranded DNA templates. Two different primers are typically included in the
reaction mixture: one for each of the two single-stranded complements
containing the target region. During this step, the polymerase binds to the
primer-template hybrid and begins DNA formation. - Elongating (@72°C)
Under optimal conditions ( at each extension/elongation step, the number of
DNA target sequences are doubled. With each successive cycle, the original
template strands plus all newly generated strands become template strands for
the next round of elongation, leading to exponential amplification of
the specific DNA target region. - repeat
-> duplicates DNA
As a rule of thumb, at their optimal temperature, most DNA polymerases polymerize a thousand bases per minute.
How does Agarose Gel Electrophoresis work?
To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode.
Explain Sanger Sequencing
4 different runs. Each run contains the same DNA different base. Gel electrophoresis is used to separate reads increasing in size in each lane.
The Sanger sequencing method consists of 6 steps:
(1) The double-stranded DNA (dsDNA) is denatured into two single-stranded DNA (ssDNA).
(2) A primer that corresponds to one end of the sequence is attached.
(3) Four polymerase solutions with four types of dNTPs (dNTPs: A, G, C, and T) but only one type of ddNTP are added.
(4) The DNA synthesis reaction initiates and the chain extends until a termination nucleotide is randomly incorporated.
(5) The resulting DNA fragments are denatured into ssDNA.
(6) The denatured fragments are separated by gel electrophoresis and the sequence is determined.
Explain Nanopore Sequencing
Enables direct, real-time analysis of long DNA or RNA fragments by driven through a protein nanopore.
It works by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore, and the molecule bridges the pore. The resulting signal is decoded to provide the specific DNA or RNA sequence, as the amplitude is specific for each of the four bases.
WHAT IS RNA & how it is different to DNA?
Ribonucleic acid. Only one single strand and uracil replace thymine as a complement to adenine. It is essential in various biological roles in coding, decoding, regulation and expression of genes.
WHAT IS Transcription & how does it work?
First, of several steps. Is the process of making an RNA copy of a gene frequency. This copy called messenger RNA leaves the cell nucleus and enters the cytoplasm. Where it directs the synthesis of the protein, which it encodes.
WHAT IS Translation & how does it work?
The next step is after transcription. Here the ribosome is in the cytoplasm or endoplasmatic reticulum and synthesizes proteins. Entier process is called gene expression.
What is southern blotting & northern blotting?
southern blotting & northern blotting are used to determine the identity, size and abundance of specific DNA or RNA(northern) sequences. To do so: DNA/RNA is isolated and gel electrophoresis, then a membrane is transferred to a labelled probe incubation and then target detection.
How many amino acids are used in proteins, and what are their differences? How are they connected?
20! They are classified as essential and non-essentials amino acids. They differ by the structure of the side chain, but all have another atom bonded to the central atom known as the R group.
How are proteins made?
DNA is first transcribed into RNA and then RNA is translated into a protein.
How do enzymes work?
- Enzymes and substrates are in the same area. Some have more than one substrate molecule.
- Substrate binds to a region on the enzyme called the active side.
- Reaction occurs resulting in the new product catalysis happens
- The enzyme releases product.
What is an antibody and where does it come from?
Are Y-shaped proteins used by the immune system to identify and neutralize foreign objects (bacteria, virus) they recognize antigens. They are produced by specialized white blood cells. b CELLS
What is an ELISA and how does it work?
- Antibody coating
- Protein captured
- Detection antibody added
- secondary enzyme linked to an antibody
- Addition of substrate (colourimetric, fluoresence)
- Analysed reflection or fluorescence
How are Antibodies made?
b-cells displaying many different antibodies -> exposure to something foreign. B-cells displaying binders are activated and start to produce soluble antibodies -> antibodies bind foreign “thing” and mark it -> disease is eaten up by macrophages
How does an Electrochemical gas sensor work and what is it used for?
- chemical reaction -> change in charge
How?
1. Target gas enters into working measuring electrode
2. chemical reaction (ions are formed). Electrons travel on an outer circuit to counter the electrode and Ions through electrolyte
3. recombine with ions
4. more gas at the measuring electrode = more electrons = more current flow
Use?
1. Detection of single gas like NO, O2, CO2, SO2
2. Monitoring of ambient
3. Alcohol test
4. Anaesthesia
5. Monitoring/ Disease Detection
What is a CCD sensor?
The CCDs (Charged-coupled device) are sensors based on an array of passive photodiodes which integrates charge during the exposure time of the camera. The charge is then transferred to common electronics which reads the accumulated charges of the different pixels and translates them in voltages.
How to measure dissolved gas concentration in liquids
and when is it used?
Clark cell
Polarization voltage applied (~500mV) -> O2 diffuses through membrane
How?
Chemical reaction at anode and cathode sensor measures current
1. ~ pO2 (partial pressure)
2. correct for system pressure
3. via Henrys Law: conc in mg/L
Higher dissolved O2 (DO) -> Lower fluorescence duration
- Excitation led puts dye in an excited state -> emitting duration detectable <- fluorescences
- Phase shift depends on oxygen partial pressure for low dissolved oxygen -> colourimetric method timing crucial
Use?
Checking oxygen dissolved in the blood
How does skin colourimetry work, what is measured and what is it used for?
How?
Light source - one or multiple different angles possible - often LED or Halogen lamps - white light (broad spectrum)
Spectroscopy: Array of photodiodes (360 - 700 nm)
Three Filters: Tristimulus calorimetry: Only specific lambda measured - sensor often XYZ data
What?
- most basic: CIELAB color space system (3D cartesian space)
-> 3 parameters l, a, b* -> plotted 3D
-> allows quantification and comparison of data
Use?
- Demand for quantitative and objective skin research tools -> results correlate with pigmentation and erythema
- Early detection of pathological conditions -> risks like cancer and indicating treatment response and disease progression
- Rapid and easily accessible non-invasive diagnostic tool
Explain Laser-Doppler-Anemometry: how doe sit work, what are the components and what is measured?
- measures velocity in transparent or semi-transparent fluid flows absolute and linear with velocity - requires no pre-calibration
Non-intrusive measurement, high accuracy, high spatial resolution, and tracer particles are required
-velocity: rate and direction of object movement - to almost all industrial and natural flows are turbulent
Optical principle
particle passes through the intersection of coherent laser beams scattered light is received by the detector
- has both components
- interfere with the surface of the detector
-produces pulsating light intensity as particles move through ( due to changes in the optical pathlength of components)
Fringe model
- it is assumed that the intersecting beams form a fringe pattern of high and low intensity
-while passing through the scattered light fluctuates in intensity with frequencies equal to the velocity of the particle divided by the fringe spacing
Bragg cell /frequency shift
- particles moving in forward or reverse direction produce an identical signal and frequency -> frequency shift -> the interference fringes appear to move at shift frequency -> allows to distinguish negative velocities
- Acusto-optical moderator -> requires a signal generator (typical 40 MHz) -> frequency is increased by shift, correction of the beam through an additional prism
