Biochemistry Flashcards
Describe entropy
a thermodynamic quantity representing the unavailability of a system’s thermal energy for conversion into mechanical work, often interpreted as the degree of disorder or randomness in the system. Disorder is spontaneous, can only increase. Reorder requires energy.
How do cells adhere to the 2nd law of thermodynamics?
How do cells maintain order in their cells?
- Non living things become disordered
- Living things maintain and generate order
- Living cells take energy from outside (e.g. the oxidation of food) and utilise it to generate order
- This energy fuels all the processes necessary for life
What is catabolism and anabolism?
By serving as energy shuttles, activated carrier molecules perform their function as go-betweens that link the breakdown of food molecules and the release of energy (catabolism) to the energy requiring biosynthesis of small and large molecules (anabolism)
What is oxidation and reduction?
In oxidation/reduction reactions, one chemical is oxidized, and its electrons are passed to another (reduced) chemical. Such coupled reactions are referred to as redox reactions
Descibe how enzymes function
Enzymes are biological catalysts. Enzymes are not consumed during a reactionEnzymes are very selective and generally only catalyze one type of reaction. When an enzyme is applied to a system that is undergoing a reaction - THE ACTIVATION ENERGY prevents the reaction occurring spontaneously. A catalyst (enzyme) lowers the activation energy. Enzymes exert their catalytic influence by forming a complex with the substrate, this lowers the activation energy required for molecule A (substrate) to be converted to molecule B (product). The enzyme is unaltered during this process
Describe the Michaelis and Menton theory of enzyme kinetics
Describe enzyme coupling
Like a train that gets the carriage over the hill, an exergonic (catabolic) reaction can “pull” an endergonic (anabolic) reaction along to its destination (products)
Energetically unfavourable reactions can be driven by a second reaction that is energetically favourable.
An example of a coupled reaction: Glucose to Glucose-6-phosphate. (hexokinase enzyme)This phosphorylation requires an energy input, and will not occur spontaneously.
ATP provides the energy and the phosphate group
The free energy released by the conversion of ATP to ADP+P+ is far greater than the energy required for the phosphorylation of glucose so, when the two reactions are coupled together, the phosphorylation of glucose goes ahead
Describe what ATP is
A molecule which contains three phosphates held together by high energy bonds.
When the 3rd phosphate is cleaved, leaving ADP, energy is released to drive anabolic reactions (same for 2nd phosphate, leaving AMP)
Conversely, energy is required to add these phosphates, which comes from catabolic reactions, such as the oxidation of food
What are carrier molecules?
A molecule that plays a role in transporting electrons through the electron transport chain. Carrier molecules are usually proteins bound to a nonprotein group; they can undergo oxidation and reduction relatively easily, thus allowing electrons to flow through the system.
Describe what a metabolic pathway is
A metabolic pathway involves the step-by-step modification of an initial molecule to form another product.There are many reactions and intermediates. These are involved in catabolic and anabolic processes.
What is meant by negative feedback in metabolic pathways?
Feedback inhibition is when a reaction product is used to regulate its own further production. Cells have evolved to use feedback inhibition to regulate enzyme activity in metabolism, by using the products of the enzymatic reactions to inhibit further enzyme activity.
What is metabolism?
Catabolic and anabolic reactions together constitute the cell’s metabolism. In particular, the conversion of energy present in food into energy required to drive all the processes needed to maintain life. We need energy to survive. Cells use energy to: Perform mechanical work: muscle contraction, cell division. Synthesises molecules: proteins, lipids and carbohydrates.Transport ions and molecules inside and between cells: information transfer in nerve cells (neurons). What is the link between the oxidation of foodstuffs and these energy-requiring activities, the answer is the phosphate compound adenosine triphosphate (ATP). Phosphoanhydride bonds are hydrolysed to release energy. Energy from the oxidation of food is used to reform the bonds ie ADP is continuously recycled back to ATP
How do we produce ATP?
Reduced nucleotides, produced by catabolic processes, are used to fuel anabolic processes indirectly (via ATP), or directly
What is glycolysis?
Glycolysis is the metabolic pathway that converts glucose C₆H₁₂O₆, into pyruvate, CH₃COCOO⁻, and a hydrogen ion, H⁺. The free energy released in this process is used to form the high-energy molecules ATP and NADH. Glycolysis is a sequence of ten enzyme-catalyzed reactions. It is an anarobic pathway and it occurs in the cytoplasm.
Describe the energy requiring stage of glycolysis
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Step 1. Phosphorylation. A phosphate group is transferred from ATP to glucose, making glucose-6-phosphate. Glucose-6-phosphate is more reactive than glucose, and the addition of the phosphate also traps glucose inside the cell since glucose with a phosphate can’t readily cross the membrane. (ATP USED)
Step 2. Isomerisation. Glucose-6-phosphate is converted into its isomer, fructose-6-phosphate.
Step 3. Phosphorylation. A phosphate group is transferred from ATP to fructose-6-phosphate, producing fructose-1,6-bisphosphate. This step is catalyzed by the enzyme phosphofructokinase, which can be regulated to speed up or slow down the glycolysis pathway. PFK is a key regulator, it is inhibited by high concentrations of products (ATP and citrate). (ATP USED)
Step 4. Cleavage. Fructose-1,6-bisphosphate splits to form two three-carbon sugars: dihydroxyacetone phosphate DHAP and glyceraldehyde-3-phosphate. They are isomers of each other, but only one—glyceraldehyde-3-phosphate—can directly continue through the next steps of glycolysis.
Step 5. Isomerisation. DHAP is converted into glyceraldehyde-3-phosphate. The two molecules exist in equilibrium, but the equilibrium is “pulled” strongly downward, in the scheme of the diagram above, as glyceraldehyde-3-phosphate is used up. Thus, all of the DHAP is eventually converted.
Describe the energy producing stage of glycolysis
Step 6. Oxidation/Reduction.Two half reactions occur simultaneously: 1) Glyceraldehyde-3-phosphate (one of the three-carbon sugars formed in the initial phase) is oxidized, and 2) NAD is reduced to NADH The overall reaction is exergonic, releasing energy that is then used to phosphorylate the molecule, forming 1,3-bisphosphoglycerate. (TWO NADH GENERATED)
Step 7. Phosphorylation. 1,3-bisphosphoglycerate donates one of its phosphate groups to ADP, making a molecule of ATP and turning into 3-phosphoglycerate in the process. (2 ATP GENERATED - aresenic uncouples phosphorylation of ATP)
Step 8. Isomersation. 3-phosphoglycerate is converted into its isomer, 2-phosphoglycerate.
Step 9. DImerisation. 2-phosphoglycerate loses a molecule of water, becoming phosphoenolpyruvate, PEP is an unstable molecule, poised to lose its phosphate group in the final step of glycolysis. Enzyme enolase is inhibited by flouride.
Step 10. Phosphorylation. PEP donates its phosphate group to ADP making a second molecule of ATP. As it loses its phosphate, PEP is converted to pyruvate, the end product of glycolysis. (2 ATP GENERATED)
What are the net products of glycolysis?
What happens NADH in glycolysis?
If oxygen is present the NADH is re-oxidised to NAD+ by the electron transport chain. However, glycolysis occurs in the cytoplasm and the ETC is found in the mitochondria, and NADH cannot transverse the mitochondrial membrane. Therefore, the hydrogens and electrons of each NADH are transferred to glycerol phosphate, which can transport across the membrane. Here glycerol phosphate reacts with FAD to produce FADH2, and results in the formation of 2 ATPs per NADH (ultimately 4 ATPs are produced from the 2 NADH molecules)
Describe fermentation
When oxygen supply is limited, pyruvate is reduced to lactate (lactic acid)
Pyruvate + NADH + H+ -> Lactate + NAD+ (latacte dehydrogenase catalyst)
Glucose -> Ethanol + CO2 + 210 kJ (plants)
Glucose -> Lactate + 150 kJ (animals)
Glucose -> 6CO2 + 6H2O + 2880 kJ
This is known as fermentation.The NAD+ produced allows glycolysis to proceed, the only source of ATP in anaerobic conditions
Describe the cinical relevance of fermentation
Ferentation yields much less energy than complete oxidation.Provides a short-term solution. If oxygen becomes available lactate is converted back into pyruvate
Oxygen debt: Amount of extra oxygen required to remove the harmful effects of anaerobic respiration
Usain Bolt has a low oxygen debt after a run, and requires fewer breaths to restore the oxygen required to convert lactate back into pyruvate
If oxygen is limited, lactic acidosis can develop, ultimately results in cell death
- Lung / heart problems cause hypoxia
- Low blood pressure leads to poor tissue perfusion with blood, so oxygen doesn’t get to tissues
- Hypoxia and hypotension (and especially both) lead to anaerobic respiration and lactic acidosis
Characterised by low pH (<7.35) and lactate >5mmol/L
This will continue until tissues are oxygenated by improving blood oxygen and blood pressure. Lactic acidosis is an underlying process of rigor mortis. Muscle tissue of the deceased resort to anaerobic respiration and significant amounts of lactic acid released. This causes a drop in pH which interferes with ATP production and causes the muscles to grow stiff, as the actin-myosin bonds cannot be released
Describe pyruvate translocation
Acetyl CoA is a key molecule that links the metabolism of sugars, proteins and fats. Acetyl-CoA is an activated 2C acetyl unit, which can be completely oxidised to CO2.
Describe the TCA cycle
Complete oxidation of the carbon atoms of acetyl CoA by the 8 step enzyme controlled TCA process:
Four oxidation steps
Each turn of the cycle produces:
1 GTP, 3 NADH, 1 FADH2, 2 CO2 (waste)
Remember: Each molecule of glucose generates two molecules of pyruvate/acetyl CoA, so as the cycle turns twice for each glucose molecule it provides:
2 GTP, 6 NADH, 2 FADH2, 4 CO2
Describe amino acid families and structure
20 amino acids – with 20 different side-chain groups (R). 11 can be synthesised by humans. 9 cannot – ‘essential’ amino acids. Dietary protein is digested into amino acids
Describe essential and nonessential amino acids
Describe some of the uses of amino acids
What is meant by a ketogenic or glucogenic amino acid?
Glucogenic: The carbon skeletons are degraded to pyruvate or TCA cycle intermediates, which are precursors for glucose synthesis (gluconeogenesis) or they can be converted to glycogen or fatty acids for storage. They can also be catabolised for energy in the TCA cycle.
Ketogenic: Carbon skeleton degraded to acetyl-CoA or acetoacetate. Ketogenic amino acids can be catabolised for energy in the TCA cycle or they can be converted to ketone bodies or fatty acids, they cannot be converted to glucose.
Give a few examples of glucogenic and ketogenic amino acids
Describe the origin or phenlyketonuria
Phenylketonuria is caused by problems with phenylalanine metabolism. If phenylalanine cannot be converted to tyrosine (usually due to a lack of phenylalanine hydroxylase), this forces conversion to phenylpyruvate, which is not normally produced by the main pathway.
Glucogenic: Phenylalanine + O2 + tetrahydrobioterin ->Tyrosine
(phenylalanine hydroxylase) Tyrosine is then ultimately metabolised to produce fumarate (4C) a TCA cycle intermediate
Ketogenic: Phenylalanine ->Acetoacetate
Acetoacetate is a ketone body. Ketone bodies cannot be synthesised to glucose.
Autosomal recessive genetic disorder i.e both parents must pass on the defective gene. Phenylalanine (and urinary phenylpyruvate) accumulate from a few days after birth. PKU leads to mental disability if untreated. Newborns are screened for PKU as one of the tests carried out using the heel prick blood sample (also includes Medium chain acyl CoA dehydrogenase deficiency (MCADD).
Treatment: Restriction of dietary phenylalanine and the artificial sweetener Aspartame (NutraSweet) -Dipeptide of aspartatic acid/phenylalanine. Supplement with Phenylalanine-free amino acids. Supplement tyrosine. Outcome excellent if treatment is started shortly after birth. If treatment delayed or the condition remains untreated, brain damage will occur
Describe amino acid catabolism
Describe step 1 of the urea cycle
Describe step 2 of the urea cycle
Describe the products, reactants and location ofeach step of the urea cycle
Describe the structure of bases
Describe nucleotide synthesis eg purines
Nucleotides are a base + five-carbon sugar (either ribose or 2-deoxyribose) + phosphate group. We obtain minor amounts of nucleotides from diet, but depend mainly on endogenous synthesis and recycling. Uric acid is excreted by kidneys into urine. Elevated serum uric acid level is called hyperuricaemia. Uric acid has low water solubility. Uric acid can form stones in kidney collecting ducts – accounts for 5%-10% of kidney stones
Describe treatment methods of gout
Describe purine salage and its clinical relevance
Lesch-Nyhan syndrome is a rare inherited X chromosome-linked recessive disorder where there is a complete loss of HGPRT activity. Symptoms include gout and neurological symptoms.The neurological effects are caused by the loss of supply of purine nucleotides from the salvage pathway, rather than by uric acid accumulation.(Lesch-Nyhan first identified by Michael Lesch, a medical student, and his mentor, paediatrician Bill Nyhan in 1964)
Describe lipid transport in the cell
What are triglycerides?
The term fat refers to molecules called triglycerides. They are digested by lipoprotein lipase producing free fatty acids and glycerol(3 fatty acids for each glycerol). Fatty acids are unbranched hydrocarbon chains with a carboxyl group at one end. Variable number of carbon atoms – 16 and 18 most common.
Describe triglyceride storage
Fatty acids are stored in the body as fat (triacylglycerol/triglyceride), predominantly in adipose tissue (adipocytes).This provides a more efficient fuel than glycogen. The energy value of 15 kg fat is equivalent to 100 kg hydrated glycogen. Fatty acids are taken up by adipocytes, activated, and used for triglyceride synthesis.
Decribe fatty acid mobilisation
Hormone sensitive adipose tissue lipase (HSL) released when body needs to mobilise energy stores. Regulates release of fatty acids from stored triglycerides in adipose tissue. These can then enter b-oxidation to provide energy. Most cells (except neurons and erythrocytes) can generate energy from fatty acids, in fact, heart and skeletal muscle prefer fatty acids to provide their energy. Energy released via b-oxidation. Occurs in mitochondria. Before oxidation, the fatty acid is activated to fatty acyl-CoA in the outer mitochondrial membrane.
R-COOH + CoA + ATP + H2O → R-CO-CoA + AMP + PPi + 2H+
Describe the process of B-oxidation
Called b-oxidation, because it is the b carbon atom on the fatty acid that is oxidised. 4-step cyclic process, taking off two carbons each cycle. One cycle of b-oxidation releases one molecule of acetyl-CoA + reduced nucleotides (FADH2 and NADH).
Energy released from the complete oxidation of C16 fatty acid: By shortening the fatty acid by 2 carbons yields 1 FADH2 + 1 NADH + acetyl CoA. This occurs 7 times and yields 7 FADH2 + 7 NADH + 8 acetyl CoA
(Each FADH2 yields 2 ATPs (7x2 = 14)/(Each NADH yields 3 ATPs (7X3 = 21)/(Each acetyl CoA yields 12 ATPs (8x12=96) = Total ATPs produced = 14+21+96=131
But 2 high-energy phosphate bonds consumed in the activation of fatty acid (AMP and PPi)
Net = 129 ATPs produced from C16 fatty acid
What is MCAAD?
MCADD is a rare genetic condition where a person has problems breaking down fat to use as an energy source, and is inherited in an autosomal recessive manner. Subjects must rely on glucose for energy. Life-threatening. Newborn screening implemented in N Ireland since August 2009.
Describe ketone bodies in lipid metabolism
Ketone bodies enter the blood and travel to other tissues where they can be oxidised to provide energy. Ketone bodies can then be converted back to acetoacetyl-CoA and then acetyl-CoA (TCA/Krebs cycle). The acetyl-CoA produced can enter the TCA cycle and produce more reduced nucleotides
If excess acetyl-CoA is present, acetoacetyl CoA can be converted to ketone bodies (acetoacetate, b-hydroxybutyrate, acetone). Occurs in liver mitochondria. Known as ketogenesis. Important during fasting and stimulated in diabetes.
Acetoacetate decarboxylated to acetone if not needed for energy. Can give a characteristic smell on the breath during fasting, and sometimes in diabetes
Describe fatty acid synthesis
Describe activation in lipogeneis
Describe elongation in lipogenesis
Fatty acid synthase adds two carbons at a time from malonyl-Co A to the growing fatty acid carbon chain, with the loss of carbon dioxide. This is why most naturally-occurring fatty acids have an even number of carbons.
Decribe termination in lipogenesis
Palmitic acid (palmitate) is a 16-carbon saturated fatty acid and is the maximum length that can occur using this enzyme complex. Following activation to palmitoyl-CoA, this fatty acid can be used to make other longer-chain fatty acids – 18C is the most common – it can also be used to make unsaturated fatty acids.
Describe the differences in fatty acid synthesis and breakdown
Describe some of the key features of cholesterol
Another important specialised biological lipid is Cholesterol. Important component of cell membranes. Component of lipoproteins. Precursor for synthesis of bile acids/bile salts. Steroid hormones. Fat-soluble vitamins, such as A, D, E & K.
Describe cholesterol synthesis
All cells can synthesise cholesterol. Liver synthesises the most (20-25%). All 27 carbons are derived from acetyl-CoA. Synthesis occurs in cytoplasm and ER. HMG-CoA reductase is the rate-limiting step. This enzyme is regulated by transcription. Cholesterol homeostasis maintained because: High cholesterol levels result in decreased HMG-CoA reductase transcription - causes reduced cholesterol production. Low cholesterol levels – increased HMG-CoA reductase transcription – causes increased cholesterol production
Describe the function of statins
