Cell Biology Flashcards
Groups at beginning and end of a polypeptide
First: NH3+ Last: COO- group.
Groups binding in disulfide bridges
Two cysteine groups (either from 2 different polypeptides or 2 on the same)
Mechanism of methylation in proteins
NH2 groups of lysine and Argenine
Secondary structure of protein bonds
Alpha helix: hydrogen bond between O and H of same polypeptide . 3.6 residues Beta pleated sheets: hydrogen bond between different polypeptides. Polypeptides can be parallel or antiparallel.
Bonds in the collagen triple helix
H bonds between 3 chains forming a triple left handed helix. Between glycine, proline and hydroxy proline.
Example of protein with high B sheers and properties
Fibrillation proteins - high tensile strength, no elasticity
Forces that stabilize protein structures (1 covalent, 4 non covalent)
Hydrogen bonds, electrostatic interactions, vander waals forces, hydrophobic effect Disulfide bridges
Why proteins can denature easily
Low amount of stabilization energy from all of the different interactions
Induced fit model of enzymes
Enzyme and substrate combine to change the shape of the substrate, so that it is more unstable and ready to change.
Reaction of lactate dehydrogenase
Pyruvate fo lactate using 1NADH and H+
Oxidoreductase enzyme example and function
Lactate dehydrogenase Transfer of H atoms and electrons
Transferase example and function
Alanine aminotransferase Catalyze transfer of functional groups
When is Km equal to the substrate concentration in the Michael Menton equation?
When the reaction velocity is at half of its maximum (ie. when V= Vmax /2)
What is the meaning of Km
The smaller km value, the higher the affinity between substrate and the enzyme
Meaning of Kcat
How many molecules of of substrate get converted to product by the enzyme in a given amount of time at saturated substrate concentration.
In the lineweaver Burke plot, 1/ Vmax is the…
Y intercept
In the lineweaver Burke plot, -1/Km is the…
X intercept
How malonate works as a competitive inhibitor
Competes with succinate for active sites of succinate dehydrogenase
How competitive inhibitors later km and vmax
Km: they increase km (decrease substrate affinity) Vmax: no effect on max velocity of reaction
Effect of non competitive enzyme on km and Vmax
Km: no change because affinity for substrate does not change Vmax: decreases because max velocity decreases with non competitive inhibitor
Explain control of angiotensin production for heart disease as an example of clinical use of enzyme inhibitor
In heart disease where blood flow is reduced, excess angiotensin would be produced causing too much vasoconstriction and reabsorltion. ACE inhibitor can be used to stop the formation of angiotensin
Example of allosteric regulation of the fructose6 phosphate to fructose 1,6 biphosphate by phosphofructokinase
+ allosteric : AMP - allosteric : ATP and citrate
Covalent modification of enzymes example of when it promotes and inhibites an enzyme.
Promotes: glycogen phosphorylase phosphorylated by addition of phosphate to Serine Inhibited: glycogen synthase phosphorylated and hence deactivated by addition of phosphate to serine residue
Amino acid on which following covalent modifications occur: Adenylylation Uridylylation ADP-ribosylation Methylation
Adenylylation: tyrosine Uridylylation: tyrosine ADP-ribosylation: arg, gln, cys Methylation: glutamine
Protein activated in cAMP pathway
Adenyl cyclase
Reaction triggered by adenyl cyclase
ATP to cAMP
2 things PKA phosphorylated
Enzyme in cytoplasm and CREB, which regulates transcription
First molecule activated by G protein in the inositol triphosphate pathway
Phospholipase C
Action of phospholipase C
Inositol phospholipid into IP3 and DAG
Action of IP3
Binds to endoplasmic reticulum and causes release of calcium
Role of DAG
Binds with calcium to protein kinase C and activated protein.
Receptor tyrosine kinase mode of action
- Two RTK bind to a ligand and come together to form a cross linked dimer. 2. Activated tyrosine kinase 3. Cross phosphorylation: the RTK phosphorylated the tyrosine of the other RTK. 4. Once phosphorylated, proteins containing an SH2 domain can bind to the tyrosine. 5. Protein gets phosphorylated
Actin filaments
- associated proteins
- monomers
- structure
- assembly and dissasembly
Protein: actin binding proteins
Monomers: G-actin (globular actin)
Structure: Polarised double helix
- assembly: monomers added from both ends, faster on + end. Uses ATP to form and releases ADP when dissasembling
Intermediate filaments
- associated proteins
- monomers
- structure
- assembly and dissasembly
Monomers: individual intermediate filament proteins
Structure: dense around nucleus, extending into the periphery
Assembly and dissasembly:
Microtubules
- associated proteins
- monomers
- structure
- assembly and dissasembly
- microtubule associated proteins
- tubulin monomer (alpha and beta subunits)
- structure: one + one - side because of alpha and beta. long stiff hollow tubes. 13 colomns of tubulin
- uses GTP for assembly. From centrosome (negative) to periphery
Example of actin filament
cilia in gut
example of intermediate filament function
stabilize shape of axons
Meshwork around the cell nucleus to hold it in position
Cell junctions
Example of microtubule function
Anchoring of organelles within the cell (RER, SER…)
DNA
The steps of actin based movement
Cell pushes out protrusion at the front due to actin filaments polymerizing in that direction.
Protrusions of F-actin (filaments) adhere to the surface cell is moving through and the cell pulls against these anchorage points to move forwards, and actin depolymerizes at the back.
How actin plays a role in lamellipodia or filopodia touching down on a surface
Actin creates the connection between focal adhesions (integrin-containing complexes connecting the cell to surface) and the rest of the cytoskeleton. Allowing for motility, transfer of info…
How the microtubule-associated-protein, dyenin, plays a role (2) in movement.
How kinesin plays a role too.
It initiates the sliding along one another, causing cilia to bend and move stuff.
Kinesin and dyenin move vescicles along the microtubules (kinesin moves it towards + end periphery and dynein moves it towards - end nucleus).
What is a processive motor protein and how it helps with the cycle
processive motor proteins like kinesin stay attached to the filament they are moving along (unlike myosin) so they can go for long distances.
Examples of cytoskeleton related therapeutics
Chemotherapeutic agents that can destabilise microtubiles or stabilise them, inhibit cell division.
How listeria bacteria hijacks the actin cytoskeleton
Affinity for glucose of GLU-1 to 5
How glut 4 is activated by insulin
Insulin causes translocation of glut 4 transporter to membrane, allowing for glucose uptake
Max size of cell
50um
How do specialised cells overcome issue of surface area
Giant multinucleated cells
thin processes (axons)
gap junctions
Golgi apparatus what it does to carbohydrates and lipids and other functions
Modifies N-linked carbohydrates
Glycosylates O-linked carbohydrates and lipids
Creates lysosomes, transports lipids
what do perixosomes do
What zellweger syndrome and adrenoleukodystrophy are in relation to perixosome
detoxification
phospholipid synthesis
Oxidation of very long chain fatty acids (VLCFA)
H2O2 degradation
Zelleweger: no perixosome
Adrenoleukodystrophy: affect protein that import VLCFA into perixosome
Lysosome function
Hydrolises major cellular macromolecules, using low pH
What is the anomeric carbon in a glucose ring molecule
The carbon attached to the original carbonyl group in cyclic form (linear structure)
Alpha vs beta glucose
Bond that binds to alpha glucoses
Alpha 1,4 glycosilic bond
Reaction catalysed by lactase
Issue with undigested lactose
Lactose to galactose and glucose
If you don’t digest it, intestinal bacteria does and produces a lot of CO2 causing bloating and diahrrea
Difference between ribose and deoxyribose
Structure of nucleotide and DNA
DNA: sugar phosphate backbone. nucleotides boud by hydrogen bonds
Structure of ATP
Types of lipids and structure (4)
TAG: triglycerides have 3 fatty acid chains bount to a glycerol backbone via ester bonds. Used for energy storage
Fatty acids: Long chain C-H chains ending with carboxyl group. Can be saturated and unsaturated (double bond). Used for energy.
Phospholopids and glycolipids: glycerol + 2 FA and phospholipds also have phosphate containing group. Make up membrane
Steroids: multi ring structure (e.g. cholesterol). Used for hormones and membrane stability
Basic structure of amino acid and bond
Peptide bond between C and N.
Classify as polar or non polar
Difference in membrane composition:
Plasma membrane
Outer/ inner mitochondrial membrane
Nuclear membrane
Basic structure of a phospholipid
Polar head group can be serine, cholne, ethanolamine, inositol
What is sphingomyelin and its structure?
Sphingomyelin: a membrane lipid mostly found in the myelin sheath of neurons. It is made up of 3 parts:
- one fatty acid chain (like in normal phospholipid)
- a sphingosine group
- phosphocholine polar head group
1 and 2 can be grouped as a ceramide
Effect of the following on membrane fluidity:
Short chain fatty acids
Short chain fatty acids: increase fluidity (reduced interactions)
Unsaturated fatty acids: increase fluidity (reduced London forces)
Cholesterol: decreases fluidity (restricts movement of polar heads)
Describe the following proteins as their type of interaction with the membrane and the bonds that secure these interactions
E.g. anchored membrane: alkaline phosphatase (bound to surface glycolipid) or RAS (fatty acyl anchored protein)
E.g. peripheral proteins: spectrin (interacts with membrane protein like ankyrin) and phospholipase A2 binds to bilayer to cleave fatty acids from phospholipids
Action of phospholipase enzymes on the phospholipids
They free fatty acid tail from polar head at different points:
