Lecture 3 and 4 Flashcards
What is the difference between thermodynamically and kinetically stable?
- A substance is thermodynamically stable when it has the lowest possible Gibbs free energy. This means that a reaction to a different state is not spontaneous.
- A substance is kinetically stable if it has a high activation barrier (delta E) that prevents it from converting to a more stable state quickly. The reaction could be spontaneous, and even thermodynamically unstable, but if it has a huge energy barrier, it will proceed slowly, or not at all.
What does the enzyme pyruvate dehydrogenase do?
Pyruvate dehydrogenase converts pyruvate into acetyl-CoA, which enters the citric acid cycle.
Where in the cell does glycolysis occur?
In the cytoplasm.
What is the net yield of glycolysis? (Give the reaction)
Glucose + 2 NAD+ + 2 ADP + 2 Pi –> 2 pyruvate + 2 NADH+ 2 ATP
How does flux make sure the reaction steps of glycolysis stay favourable?
Flux through glycolysis ensures that concentrations of substrates and products are kept at a certain value (more substrate than product, k < 1) making delta G positive, even though delta G0 may be negative.
What is the reaction of the citric acid cycle?
Acetyl-Coa + 3 NAD+ + FAD + GDP –> CoA + 3 NADH + FADH2 + GTP + 2 CO2
What are the consequences of an absence of oxygen to the production of energy?
- No more ATP production through oxidative phosphorylation.
- Subsequently, no regeneration of NAD+, so no reducing power for glycolysis or the citric acid cycle.
Consequence: complete halt of ATP production
How do plants store fats and polysaccharides? How do animals do this?
- Plants: starch granules and fat droplets (in chloroplasts)
- Animals: glycogen granules (in liver cells) and fat droplets (in fat cells)
How are single sugar subunits formed from glycogen?
- Glycogen phosphorylase releases one sugar subunit and adds a phosphate group. The product is glucose-1-phosphate.
- Phosphoglucomutase transfers the phosphate group to another carbon of the glucose. The product is glucose-6-phosphate, which is the substrate of enzyme 2 in glycolysis.
Name the amino acids that have positively charged side chains:
- Positive side chain (PH=7): Arg, Lys, His
Of which isomer do proteins solely consist?
Proteins consist exclusively of L-amino acids.
Name the four levels of structural organization of proteins and an example for each one.
- Primary structure: amino acid sequence
- Secondary structure: alpa-helices and beta-sheets, formed by the polypeptide backbone (!)
- Tertiary structure: 3D folding pattern of protens due to side chain (!) interactions.
- Quartenary structure: Protein consisting of multiple polypeptide chains. (Hemoglobin, for example)
What are two experimental methods to determine protein structure and how do they work?
- X-ray christallography: Shine an X-ray beam on a crystallized protein, the diffracted beam can be recorded as a pattern of spots. These spots can be converted into an electron density map, which is then used to construct a model of the 3D structure.
- Electron microscopy: Using an electron microscope you can get images up to the atomic scale. The obtained image is used to construct the 3D structure.
What are the three subunits of pyruvate dehydrogenase and what do they do?
- Decarboxylase: removes carboxyl group, releases CO2.
- Oxidase: remaining part of pyruvate is converted to acetyl.
- Transferase: acetyl is transferred to CoA.
What is the importance of ketone bodies and name two of them.
Ketone bodies serve as an alternative energy source for the brain and heart during periods of prolonged fasting. Examples: acetoacetate and beta-hydroxybutarate. They are derived from fatty acids and the oxidation of these molecules serves as energy source (ATP).
What are three ways in which a protein can enhance its reactivity to ligands?
- Restrict the acess of water to the ligand-binding site.
- Clustering of polar amino acid side chains. For example: clustering of negatively charged amino acid side chains enhances the proteins affinity for positively charged ligands.
- Side chains interacting with each other to form hydrogen bonds, forming reactive groups.
What are the ways in which two proteins can bind to each other?
- Surface-string
- Coiled-coil
- Surface-surface
What is Km and what does a high Km and low Km mean?
Km is the concentration of substrate that allows the reaction to proceed at one-half of its maximum rate.
* Low Km: means that the enzyme reaches its maximum catalytic rate at low concentrations of substrate and indicates that the enzyme binds to its substrate tightly.
* High km: the enzyme reaches its maximum catalytic rate at high substrate concentrations and means weak binding.
Which amino acids have a negatively charged side chain?
Negative side chain (PH=7): Asp, glu
Which amino acids have uncharged polar side chains?
Uncharged polar: Asn, Gln, Ser, Thr, Tyr
