New biophysics Flashcards
What are eukaryotic cells?
Cells with a nucleus that contains genetic material (DNA) (like animals, plants, fungi, protozoa and algae). Can be uni- or multi-cellular
What are prokaryotic cells?
Cells without a nucleus (like bacteria). Always uni-cellular
What are organelles?
Organelles are compartments within a cell with specific specialised functions. They can be membrane bound or membraneless. Each organelle can have completely different protein and ion compositions to those surrounding it.
What are organelle examples?
nuclear membrane, the Golgi Apparatus, the Endoplasmic Reticulum and the Mitochondria
What are structural features of the cell made of and what are examples of them?
The structural features of the cell can be made by lipids or proteins. Outside part of the cell is the plasma membrane (made of lipids) and microtubules and actin filaments are structural features made from proteins.
What is the genome?
entire set of DNA of an organism
What is a polypeptide chain?
A protein
What shape are viruses?
Icosahedra
What can viruses have to make them more complicated?
Lipid bilayers and surface receptors
What is a codon and what does it do?
3 nucleotides and it tells us what amino acid is going to be produced
How many amino acids are there?
20, plus start and stop codons
What is gene expression?
process by which DNA instructions convert into proteins with two key stages: transcription and translation
What are the 4 types of protein structure?
Primary, secondary, tertiary and quaternary
What is the most common type of protein structure?
Tertiary
What is roughly the volume for one base pair?
1 cubic nanometre
The volume of a container (eg a nucleus) is measured in what amounts usually?
Cubic nanometres
What is the Levinthal paradox?
The correct protein folding by a simple random search is very improbable and would take a long time and yet correctly folded proteins are common and happen relatively quickly
What is the solution to the Levinthal paradox?
Folding is not random and protein sequences contain folding pathway information.
How is the helix shape made in alpha helices?
They have a hydrogen bond every 4th amino acid connected to each other (so there’s 2 amino acids between the connected ones)
What is Gibbs free energy?
maximum reversible work that may be performed by a system at constant temperature and pressure
What is enthalpy (H)?
heat absorbed or released
What is entropy (S)?
measure of disorder in a system
What is the hydrophobic effect when considering protein folding?
causes hydrophobic residues to hide in the centre and hydrophilic residues to be pushed outwards
What does the spontaneous back-to back arrangement of a bilayer of lipids for the cell membrane look like?
The hydrophilic head groups on the outside in water (which is where they self-assemble) and the hydrophobic tails in the core of the membrane
What properties of phospholipids drives self-assembly?
The hydrophilic/ hydrophobic nature of them
What are lipids?
A broad group of naturally occurring molecules, including fats and waxes
What determines the type of structures formed of any given lipid?
The packing parameter
What is a micellar solution?
head groups facing out in a circle into water, hydrophobic tails inside into oil (oil in water)
What is a lamellar state?
planar bilayer with head groups on the outside and tails on the inside
What is an inverse solution?
tails facing out in a circle in an oil-rich environment and heads inside in a water-rich environment (water in oil)
How can lipids transition between states (eg micellar, lamellar)?
External environmental factors, like temperature
What is phase separation and what is an example of this?
A phase separates into coexisting lamellar domains, eg a lipid raft
What is lipid asymmetry (one of the mechanisms to induce membrane curvature)?
different shapes and sizes of lipids on exterior surface
What is crowding (one of the mechanisms to induce membrane curvature)?
adding molecules on exterior surface
When are cylindrical shapes of lipids (type 0) formed?
Hydrophilic and hydrophobic regions are similar size
Non-lamellar phases are what type of phase and what’s an example of this?
Non-bilayer phases and micelles
What are the 3 types of bicontinuous cubic phases?
gyroid, primitive and double diamond
What are organelles a combination of?
Lipids, proteins, nucleic acids, sugars and salts
What is an example of what the Golgi apparatus does?
Packs proteins the membrane-bound vesicles and send them to where they are required
What maintains the low pH in lysosomes?
Proton pumps and chloride ion channels
What is the cytoskeleton made out of?
Different types of polymers
Is the cell a dynamic system and what does this mean?
Yes, so its not at equilibrium and there is constant formation and disassembly
Is the cell a dynamic system and what does this mean?
Yes, so its not at equilibrium and there is constant formation and disassembly
How long does a protein take to make in its stages?
30 mins for transcription and 30 mins for translation
How does the time take to form protein into structures compare to the time it takes to make the proteins themselves?
A lot quicker
What are examples of what kinesins are used for?
Mitosis and transport of cellular cargo
What is fluorescence?
Light of an appropriate wavelength is shined on certain molecules, which will promote an electron into an excited/ higher energy state and then this will de-excite back to a lower energy state, emitting a photon as it does.
When a photon of energy equal to energy level differences is absorbed, electrons are promoted from and to what type of orbitals?
HOMO (highest occupied molecular orbital) to LUMO (lowest unoccupied molecular orbital)
How does phosphorescence occur?
photon is absorbed and electron moves up energy state then intersystem crossing occurs, which changes its spin state so it can’t move back down easily, then it does but takes longer
In extrinsic fluorescence, what is the tag also called?
Dye or label
What is photobleaching?
photon-induced chemical damage of fluorescent molecules such that it is permanently unable to fluoresce
What are the super resolution techniques?
STED and PALM
What is a FRET pair and a non-FRET pair in terms of what fluorescence you see?
FRET pair = acceptor fluorescence. Non-FRET pair = donor fluorescence
What surrounds the nucleus?
Nuclear envelope, which has pores in it to allow mRNA to diffuse in and out
What is the central dogma of cell biology?
Theory that genetic info only flows in one direction, from DNA to RNA to protein
What do capsids do?
Protects them
What is the primary structure of proteins?
linear sequence of amino acids.
What is the secondary structure of proteins?
Linear sequences of amino acids in spatial arrangements, like alpha helices and beta pleated sheets
What is the tertiary structure of proteins?
alpha helices and beta sheets combined with unstructured regions folded
What makes amino acid structures different to each other?
Different R groups (side chains)
What is the cell membrane?
outer layer of eukaryotic cell and is made of a bilayer of lipids and embedded with membrane proteins. It is a semipermeable barrier.
What are liposomes made from and what does its structure eliminate?
A flat bilayer and it eliminates energetically unfavourable edges
