ביוכימיה Flashcards
(40 cards)
which vitamin contains a Co ion?
1. Vitamin C
2. Vitamin B12
3. Vitamin B3
4. Vitamin D
- Vitamin B12
B12, also known as Cobalamin, is a vitamin that participates in very few reactions in the human body, but a deficiency in it is crucial and can result in severe diseases (neural damage u.a).
It participates in replacing a hydrogen in carbon group in the oxidisation of fatty acids (specifically odd fatty acids, which leaves a propionyl CoA, a 3-carbon molecule which cannot be transformed into Acetyl CoA). Propionyl CoA undergoes a cascade of reactions to finally become acetyl CoA and enter the Citric Acid cycle. B12 participates as cofactor in the 3rd (and final stage) of L-Methylmalonyl CoA - isomerisation to replace a hydrogen in carbon group within the molecule to create Succynyl CoA.
what is true about the native conformation of a globular protein in an aqueous environment?
1. the most stable conformation has the most free energy
2. disulphide bonds are the most prominent interaction to form a protein
3. increase in entropy is the driving force of hydrophobic interaction
in the protein
4. negatively charged AA have no negative influence on the protein
- increase in entropy is the driving force of hydrophobic interaction
in the protein
hydrophobic interactions are the most important bonds for globular proteins. The native structure of a protein is achieved when the protein’s biological function is enabled. Hydrophobic interactions occur when the protein’s hydrophobic residue are rejected in aqueous environment (which leads to increase in entropy), which results in a folding of the residue inwards towards the hydrophobic protein core, where interaction with water is minimal.
What happens in response to insulin secretion?
1. glucose in absorbed into nerve cells
2. transportation of TAG to fat cells by VLDL
3. transportation of fatty acids from fat tissue to the liver by albumin
4. gluconeogenesis in the liver
- transportation of TAG to fat cells by VLDL
Fat and its derivatives are hydrophobic, therefore they cannot dissolve and into the aqueous bloodstream alone.
2 solutions:
- linking free fatty acids to albumin to transport it to the liver
- aggregation of fatty acids and cholesterol on lipoproteins that can bind them and still remain soluble.
VLDL is the lipoprotein that supplies fats and cholesterol to body tissue. in the presence of high amount of fat and cholesterol, and when insulin signals mediate anabolic, fat preserving processes, VLDL particles unload their content in fatty tissue for preservation. when partially empty, VLDL then become LDL particles which are very rich in cholesterol
In which direction do the R group in alpha helix point?
(out/in)
Outwards
How many amino acids are there in each loop of the alpha helix?
4 AA+ 1 hidrogen
What is true about the alpha helix?
1. R groups point inwards
2. most common form is L-alpha
3. each loop of the helix contains 5 AA
4. pH can destabilise the helix
- pH can destabilise the helix
Alpha helix is a secondary structure, whose stabilising forces are mostly hidrogen bonds between the alpha amino and alpha carboxyl groups of the polypeptide core. each loop in the helix has ~ 3.7 residue and the most common form is D-alpha. the helix stability is affected among others by the R outward pointing groups that compose it. therefore, negatively charged R groups will reject each other and the helix will lose stability by certain pH values.
What molecule is essential for liver function and is exclusively dependent on the pentose phosphate pathway?
1. cholesterol
2. DNA
3. glycogen
4. glucose
- DNA
the pentose phosphate pathway is an important pathway that generates 2 important products: phosphorylates-pentose molecules which are used to create DNA bases and NADPH, which results from oxidation of glucose-6-phosphate.
different cells use these 2 products differently. For example blood cells dont synthesise DNA at all but they use NADPH to neutralise free radicals. in the liver that is regenerating very often, there is a high demand for DNA bases to generate new cells.
distractors:
1. cholesterol is important for the fluidity and flexibility of the plasma membrane but we most often receive it from our diet
3. glycogen is stored in the liver and is an important energy source, and allows liver cells to release glucose into the blood stream in states of hunger, but it is not dependant on the pentose phosphate pathway
4. glucose is not dependent on the pentose phosphate pathway and is not a product, or a reactant of it, but rather it is consumed by liver cells or released back into the blood.
what are the pentose phosphate pathway equation (oxidised)?
glucose-6-p + 2NADP + 2H2O –> ribose-5-p + 2NADPH + 2CO2 + 2H+
what are the steps of the pentose phosphate pathways
Oxidising stage:
1. dehydrogenation (by glucose-6-p dehydrogenase): glucose-6-p –> 6-phosphogluconolactone, 1 NADP receives H+ and becomes NADPH
- hydration (gloconolactonase): 6-phosphogluconolactone becomes 6-phosphogluconate, h2o loses carboxyl group and 1 free hydrogen ion released
- dehydrogenation + decarboxylation (phosphogluconate-DH): 6-phosphogluconolactone becomes ribulose-5-p, NADP becomes NADPH+CO2
Unoxidising stage:
4.
which hormone can slow down glycolysis and in what tissue?
1. liver, by insulin
2. muscle by insulin
3. muscle by glucagon
4. liver by adrenaline
- liver by adrenaline
in the liver, adrenaline activates glycogen phosphorylase (which phosphorylates cAMP) and promotes release of glucagon which break down glycogen and promotes glucose release from liver cells into the blood stream. it slows down ‘glucose-wasting’ processes (gluconeogenesis, glycolysis) and delays the release of enzymes such as insulin and glycogen synthase (also by phosphorylating cAMP)
In the Crebs cycle, which of the following enzymes promotes a redox reaction of a molecule containing 4-carbons to generate NADH?
1.Alpha-ketoglutarate-DH
2. Malate DH
3. Isocitrate DH
4. Aconitase
- Malate DH
Isocitrate has 6 carbons (isocitrate-DH oxidises it to alpha-ketoglutarate (5C) + NADH); alpha-ketoglutarate is oxidised to malate + NADH by alpha-ketoglutarate DH; malate is oxidised to oxalacetate (4C) +NADH;
What happens when haemoglobin binds O2?
The affinity od haemoglobin to O2 depends on many factors including tissue temperature and tissue pH: This is because there is a difference in the locations that haemoglobin needs to bind and offloaded, as it e.g. needs to bind O2 in the lungs (with very high affinity) and offload it in a different tissue. Therefore, the binding process is highly regulated by environmental factors
(with respect to pH- in the lungs it’s 7.6 and in the blood its 7.2 which leads to binding of o2 in the position the heme group , and the proteins will bind elsewhere).
The binding between O2 and de-oxy HG coming from body tissue to the lungs (de-oxygenated HG) leads to a conformational change from a tense (T) to relaxed (R) form. the relaxed HG can then bind other O2 molecules with higher affinity. **O2 binding is sigmoid (cooperative) binding;
What is the purpose of Creatine phosphate pool?
Muscle cells contain limited amount od ready ATP. therefore it needs a pool with a substance that can readily be converted to ATP at times of high physical effort. During physical activity creatine phosphate is broken down into phosphate (p) and creatine by the enzyme creatine kinase. the p can the be readily paired with ADP to to generate ATP.
during rest, creatine kinase (same enzyme from before) pairs p to creatine to replenish the creatine phosphate pool. therefore we can expect to observe high levels of this enzyme during rest shortly after physical activity.
What is an Exergonic reaction
Exergonic reaction is a chemical reaction where the change in the free energy is negative (there is a net release of free energy).[1] This indicates a spontaneous reaction if the system is closed and initial and final temperatures are the same. For processes that take place in a closed system at constant pressure and temperature, the Gibbs free energy is used, whereas the Helmholtz energy is relevant for processes that take place at constant volume and temperature.
Bottom line, a reaction is considered exergonic when delta G (the difference in Gibs free energy) is negative (i.e. energy is released to the environment); –> when considering the equation for Gibs free energy:
deltaG = deltaH - Temperature * deltaS , this means that H needs to be negative (or smaller than -TdS) and dS needs to be positive (to not flip the minus sign)
What does an increase in delta S (free entropy) means for a system
increase in irregularity
What does a decrease in delta H (free enthalpy) means for a system
increased stability of bonds in a the reactors
What is a Lineweaver-Burk plot?
a Graphical representation of the Michaelis Menten equation used to calculate kinetics. the y axis is 1/V0 (1/rate) and the x axis is the 1/Km. it is often used for determining the type of enzyme inhibition as it can distinguish between competitive, uncompetitive (irreversible) and non-competitive inhibitors. an uninhibited compound will go from 1/v = 0 and a negative Km to a positive low 1/v and a high 1/km (not so steep). a pure non competitive will start fro the same 0 point of uninhibited and will have a much steeper line and will have a low km at high 1/v. uncompetitive will go in parallel to the uninhibited curve but with a higher value for 1/v for the same 1/km values; competitive inhibitor will look similar to non competitive but will start from a less negative 1/km at 1/v=0.
In what stereoisomer configuration are large proteins found in nature?
a. Only L
b. only D
c. equal amounts of L and D
a. Only L
In what stereoisomer configuration are sugar molecules found in nature?
a. Only L
b. only D
c. equal amounts of L and D
b. only D
What is a Fas complex
Fatty Acid Synthase (FAS) catalyses the synthesis of Flamitate (16 saturated carbons) from malonyl CoA
What is the role of the enzyme the MAPKKK?
MAP kinase kinase kinase is a serine/threonine-specific protein kinase.
MAPKKK is responsible for various cell functions such as cell proliferation, cell differentiation, and apoptosis.
It is an mitogen-activated-protein family of 3 enzymes (kinases) that phosphorylate each other (MAPKKK phosphorylates MAPKK on serine which phosphorylates MAPK ) in a cascade. some enzymes in the family are RAF, MEK, ERK.
What is the role of glycogenin?
the primary enzyme that creates glycogen in the glucogen-genesis. It generates a primer of glucose molecules that are linked to tyrosine. It is the first step in generating glycogen
What are epimers
Epimers are type of stereoisomers that are non-mirror images and differ in spatial arrangement only at one chiral center, so they will have the same direction (L will always have L-epimers and D will always have D)
What is the source and end products of Nicine (B3)?
source : tryptophan
end product: NAD (important for the electron transport chain)
