CBS Flashcards
Cells are the fundamental units of life meaning…
- All living organisms are made of cells.
- Higher organisms are ‘communities’ of cells.
- Individual cells perform specialized functions within ‘communities’.
- Nothing less than a cell can truly be called living e.g. viruses.
Define the term cell.
A semi-independent, living unit within the body, (in unicellular organisms, completely independent) in which are found the mechanisms for metabolism, growth and replication (by division). It consists of an aqueous solution of organic molecules surrounded by a membrane.
Define the term organelle.
A subunit within a cell, with a defined structure and performing specific, integrated activities. Some are bounded by membranes, others are non-membranous e.g. ribosomes.
Define the term tissue.
An organised assembly of cells and their extracellular products which carry out similar and coordinated activities within the body (connective, lymphoid). An example is extracellular matrices.
Define the term organ.
An assembly of tissues coordinated to perform specific functions within the body (eye, ear, heart, lungs, liver).
Define the term system.
An assembly of organs with specific, related activities that share regulatory influences (e.g. respiratory) OR it may be a diffuse functional network of cells situated in many parts of the body, sharing specific activities (e.g. immune).
Define the term prokaryote.
A single-celled organism in which the chromosome is a circular strand lying free in the cell (i.e. no nucleus) and has no membranous organelles e.g. Bacteria.
Define the term eukaryote.
One or more cells in which chromosomes are enclosed in a nucleus. They typically have cytoplasmic, membrane-bound organelles, DNA divided into a series of linear chromosomes and considerable differences occur between cells within the same organism. All complex organisms (plants, fungi, animals, protozoa, algae) are eukaryotes.
Define the term virus and explain how they infect cells.
An assemblage of nucleic acid (DNA or RNA) and proteins (and often other molecules) which is parasitic on prokaryotes/eukaryotes. Viruses invade cells, subvert their protein synthesis machinery to make more viruses instead of normal cell proteins, then escape to infect other cells. Viruses are not cells or organisms in the strict sense (they lack a plasma membrane and only operate chemically within host cells).
What is the Cell Theory?
“All living things are made of cells and these arise through the division of pre-existing cells”.
What is the difference between TEM and SEM and what is their main disadvantage?
TEM = electrons go through the specimen. SEM = electrons scatter off the cell surface.
Can only evaluate dead cells.
What limits the maximum size of a cell?
Surface area and diffusion distance.
Name three ways in which specialised cells have overcome the problem of size.
- Thin processes (cytoskeleton).
- Multi-nucleated cells.
- Gap junctions.
What do organelles allow?
- Specialised environments to exist.
- Different functions to operate under different conditions.
Describe two features of a nucleus.
- Largest organelle in cells (3-10μm).
- Only organelle clearly visible by light microscopy.
What happens within the nucleolus?
- Where rDNA is transcribed.
- Where ribosome subunits are assembled.
What are the functions of SER and RER?
SER:
- Biosynthesis of membrane lipids and steroids occurs.
- Start of N-linked glycosylation.
- Detoxification of xenobiotics (mainly liver cells) (e.g. P450 system) occurs.
RER:
- Is coated with ribosomes for translation, proteins for secretion or insertion into cell membrane.
- Proteins are folded; cys-cys bridges form.
- Vesicles are budded from RER and transported to the Golgi body.
Describe the structure and function of the Golgi Complex.
The golgi is composed of 4-8 closely-stacked, membrane-bound channels (cisterna). They modify proteins delivered from RER via vesicles. They:
- Modify N-linked carbohydrates.
- Glycosylate O-linked carbohydrates and lipids.
- Synthesise/package materials to be secreted.
- Direct new proteins in vesicles to their correct compartments – acts as a sorting office.
- Transport membrane lipids around the cell.
- Create lysosomes.
What are the functions of peroxisomes?
- Detoxification
- Phospholipid synthesis e.g. plasmalogens
- Oxidation of Very Long Chain Fatty Acids VLCFA
- Enzymes which generate (and degrade) H2O2
Name two peroxisome pathologies.
- Zellweger Syndrome: the inherited absence of peroxisomes due to defects in targeting.
- Adrenoleukodystrophy (ALD): affects protein that imports VLCFA into peroxisomes.
What are the functions of lysosomes?
- To produce >50 different hydrolytic enzymes that can hydrolyse all major cellular macromolecules.
- Involved in organelle turnover/replacement – autophagy.
Name the dysfunctional organelles that cause:
- Hutchinson–Gilford Progeria Syndrome (HGPS)
- Myoclonic Epilepsy with Ragged Red Fibres (MERRF)
- Tay Sachs Disease
- Nucleus.
- Mitochondria.
- Lysosomes.
What is a unique about prokaryotes and carbohydrates?
Prokaryotes use carbohydrates in their cell walls which is unique. This is important in antibiotic synthesis.
What is glycosylation linked to?
Diabetes. One way to see how a diabetic is controlling their glucose levels is to look at the glycosylation of haemoglobin as this only happens when there is elevated glucose in the plasma.
What are aldoses and ketoses?
They are monosaccharides which contain one aldehyde group (aldose e.g. glucose) or one keto group (ketose e.g. fructose) which changes the functionality of the carbohydrate.
What causes the ring structure of sugars?
A nucleophilic attack by the lone pair of oxygen electrons of the hydroxyl group on the carbonyl carbon.
What is the difference between the α and β forms of sugars and why is this important?
The -OH group on the anomeric carbon is either down (α form) or up (β form).
This is important in polymerisation (formation of a glycosidic bond).
What makes a reducing sugar?
If the anomeric carbon is not attached to another molecule it is a reducing sugar.
What enzyme is needed to make a glycosidic bond?
Glycosyltransferase
What is the advantage of branched glycogen?
There are a large number of ends which means there are lots of sites where glycogen can be turned into glucose quickly.
Describe the digestion of glycogen in the diet.
- Salivary α-amylase causes random hydrolysis of internal α(1→4) linkages.
- Digestion is continued by pancreatic α-amylase to form a mixture of mono- and disaccharides.
- Finally maltase produces glucose to be absorbed by the intestinal mucosal cells.
What are fatty acids?
Long chain aliphatic carboxylic acids that are metabolised via the β-oxidation pathway to generate ATP.
Which amino acids must we gain from our diet?
- Threonine
- Methionine
- Lysine
- Valine
- Leucine
- Isoleucine
- Histidine
- Phenylalanine
- Tryptophan
What are the single letter amino acid codes for tryptophan, glutamate, aspartate, lysine, glutamine and asparagine?
W : tryptophan E : glutamate D : aspartate K : lysine Q : glutamine N : asparagine
What is phenylketonuria (PKU)?
Where you have defective phenylalanine hydroxylase (phe-tyr). Reduced levels of tyrosine lead to reduced dopamine and melanin production.
What are the features of a peptide bond?
It has a partial +ve charge on the O atom and a partial -ve charge on the N atom which allows peptides to form hydrogen bonds.
It is a rigid C-N bond with no rotation.
What amino acids are disulphide bridges between?
Cystines
Describe the four levels of protein structure.
1) Primary = a sequence of amino acids in a peptide chain.
2) Secondary = folding/coiling of a peptide chain (usually into a helix or beta sheet).
3) Tertiary = folded peptide chain folds upon itself.
4) Quaternary = folded peptide chains are joined together.
What amino acid will you never see in an alpha helix?
Proline
What is the backbone of an α-helix formed of?
Hydrogen bonds that form between the peptide bond carbonyl-O & H of N-H every 4th peptide.
What holds β-pleated sheet strands together?
Hydrogen bonding between the peptide chains.
What are the two types of β-pleated sheet?
Antiparallel and parallel.
What is the difference between a collagen triple helix and an α-helix?
- Collagen triple helix has a left-handed turns and contains large amounts of proline and hydroy-proline.
- α-helices are right-handed and you will never see proline in their structure.
What features do proteins with high % of β-pleated sheet have?
They have a high tensile strength but no elasticity. They include fibrillar proteins (silk fibres) and are not very common.
What does the word domain mean to a structural biologist?
A particular unit of structure that is common. Also known as supersecondary structures.
Which amino acids have residues that are charged at physiological pH?
- Aspartate and Glutamate have ionised carboxyl groups.
- Lysine and arginine have ionised nitrate groups.
What are Van der Waals forces?
The sum of the attractive or repulsive forces between molecules excluding those due to covalent bonds, hydrogen bonds or electrostatic forces.
What happens when proteins get too close to each other?
The Van der Waal’s forces cause positive nuclei to repel each other ensuring the correct distance is maintained.
Name three diseases that are caused by misfolding of proteins.
- Sickle cell disease caused by polymerisation of HbS.
- Amyloid proteins forming plaques in Alzheimer’s disease.
- Prion protein polymerisation in Creutzfeldt-Jakob disease.
Define an enzyme.
Biological catalysts which speed up the rate of a reaction without altering the final equilibrium between reactants and products.
What is the effect of an enzyme on activation energy of a reaction?
An enzyme lowers the transition state (free energy of activation) allowing a reaction to happen faster.
What is an intermediate in a reaction?
Something that may be happening during the process of A going to B. It is of high energy so is not very stable, but can be chemically isolated.
What are the six major classes of enzymes?
1) Oxidoreductases - add O2 or remove 2H
2) Transferases - transfers functional groups from donors to acceptors
3) Hydrolases - hydrolytic reactions (cleaving bonds by adding water)
4) Lyases - adding groups to C=C bonds and cleaving C-C, C-O or C-N bonds
5) Isomerases - transfer of functional groups between like molecules
6) Ligases - forms C-C or C-N bonds with ATP
What are homo- and hetero-oligomers?
- Homo = the same chain repeated many times.
- Hetero = a structure formed of multiple chains.
What is the chymotrypsin mechanism?
Phase 1:
- The enzyme creates nucleophile from serine side-chain.
- The nucleophile attacks the substrate.
- Covalent intermediate is formed with second product (PN) bonded to serine and first product (PC) is released.
Phase 2:
- The enzyme creates a nucleophile from a water molecule.
- Nucleophile attacks the covalent intermediate breaking the covalent bond to serine.
- The second product (PN) is released.
What are isoenzymes?
Enzymes with different protein structures which catalyse the same reaction. They are coded by different genes.
What is enzyme kinetics?
The study of the rate of an enzyme catalysed reaction and how the rate varies with different substrate concentrations, amounts of inhibitors, metal ions and cofactors as well as pH.
What is reaction rate?
Either: decrease in the amount of substrate per unit time
Or: increase in the amount of product formed per unit time.
What is the Michaelis-Menton reaction model used for?
It allows you to understand and quantify the velocity as a function of the substrate concentration using the individual kinetic equations.
What are the three assumptions for the Michaelis-Menton reaction model?
1) Any amount of substrate bound by the enzyme at one time is small.
2) The enzyme-substrate complex does not change with time.
3) Initial velocities used and concentration of product can be ignored.
What is the Michaelis-Menton equation?
V0 = Vmax x [S] / Km + [S]
Where:
- V0 = initial reaction velocity, measured as soon as the enzyme and substrate are mixed.
- Vmax = maximal velocity of an enzyme catalysed reaction (when all enzyme active sites are fully saturated).
- Km = Michaelis constant
- [S] = substrate concentration.
What happens when you plot V0?
You get a hyperbolic curve.
What does Km equal?
Half of Vmax
What does the value of Km mean in terms of affinity?
The lower the value of Km, the higher the affinity of a substrate for a particular enzyme.
What is Kcat?
The turnover number i.e. the number equivalent to the number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when the enzyme is saturated with substrate. This tells you how efficient the enzyme is.
What is the best method for comparing catalytic efficiency?
A Kcat/Km ratio. A high ratio shows that the enzyme is extremely efficient.
What is the Lineweaver-Burke plot and what is it used for?
Where you rearrange the Michealis-Menton plot to form the equation for a straight line.
This can be used to determine Km and Vmax as well as to determine the action of enzyme inhibitors (if they are competitive or non-competitive).
Why is finding -1/Km extrapolation?
Extrapolation is when you have a limited set of experimental values and you’re looking at the value that the best fitting shows you - you’re following the line of best fit to a value that doesn’t exist. This applies to -1/Km because it is impossible to have a negative substrate concentration.
What are the differences between lactate dehydrogenase in the heart and the muscle?
- Muscle has a high Kcat because muscle generates a large amount of lactate during exercise.
- Heart has a lower Kcat because if levels of lactate in the heart are as high as the muscle, you’re probably dead. Instead, it has a low Km allowing for small amounts of lactate to be removed quickly.
What is a new test developed by KCL used to detect a heart attack in A&E?
Blood test for the levels of cardiac myosin-binding protein C (cMyC). Levels increase in the blood during a heart attack.
This method is more efficient than the troponin method currently used.
What is the effect of a competitive inhibitor on Km and Vmax?
- Km increases.
- Vmax is not affected due to theoretical conditions of an infinite substrate concentration.
The curve shifts to the right.
What is the effect of a non-competitive inhibitor on Km and Vmax?
- Km stays the same.
- Vmax is lowered considerably.
What are allosteric binding sites?
They are binding sites that are different from the active site and provide a level of regulation. Effectors or inhibitors can bind here.
What is a hallmark of allosteric modification of enzyme activity?
A sigmoidal curve of substrate concentration.
Haemoglobin is an example of this.
State the typical effector, change and time required for change for the following regulator events: 1) Substrate availability; 2) Product inhibition; 3) Allosteric control; 4) Covalent modification; 5) synthesis or degradation.
See table slide 47 in Enzyme Kinetics lecture.
What is pH?
A measure of hydrogen ion concentration i.e. the acidity or alkalinity of a solution. pH is the -log of the hydrogen concentration in a solution.
What is the normal pH range of blood?
7.35-7.45
What is the living range of blood pH?
7-7.8
How do acids enter our body?
- In foods we eat
- The breakdown of proteins
- The incomplete oxidation of fats or glucose
- Loading and transport of CO2 in the blood
What regulates the acid-base balance in the body?
- Lungs
- Kidneys
- Chemical buffers
How do the lungs reduce the acidity of the blood?
By increasing the rate of breathing to expel more CO2, as long as the acidosis is not too severe.
How do buffers resist abrupt and large swings in pH of body fluids?
- Releasing H and acting as acids when the pH begins to rise.
- Binding H and acting as bases when the pH drops.
