Biochemistry Flashcards
Who is the father of biochemistry?
Archibald Edward Garrod
What is biochemistry?
The branch of science is concerned with the chemical and physicochemical processes and substances that occur within living organisms.
Define metabolism.
All chemical reactions that maintain the living state of cells and organisms.
Define anabolism and does it require energy?
The synthesis of complex molecules in living organisms from simpler ones.
It requires energy.
Define catabolism and if it requires energy.
The breakdown of complex molecules in living organisms to form simpler ones.
It breaks down molecules to yield energy.
Where does all our energy come from?
Ultimately, all our energy comes from the sun
Define redox reactions
Redox reactions are reactions where both oxidation and reduction take place.
Sketch the anabolism redox reaction.
Check in notion
What are the two terms used in anabolic reactions?
Endergonic: Reaction that requires energy to proceed
Reductive: When a reactant accumulates electrons during a reaction.
What is the electron carrier in anabolism?
NADPH + H+
Sketch the catabolic reaction
Check notion
Sketch the catabolic reaction
Check notion
What are the two terms used in catabolism regarding the reactions?
Exergonic: It releases free energy.
Oxidative: A chemical reaction occurs when a substance comes into contact with oxygen or another oxidizing substance.
What is the electron carrier in catabolism?
NADH + H+
(FADH2)
Sketch the oxidative phosphorylation in redox reactions.
Check notion
What is the energy carrier in oxidative phosphorylation?
ATP (Adenosine Tri-phosphate)
Which is the most important carbohydrate?
Glucose
What three polysaccharides have more than half of all organic carbons? In what organism can you find them?
Starch and cellulose: Plants.
Glycogen: Animals.
What is our primary energy source?
Glucose, oxidised to CO2 and H2O
What five cells require glucose as an energy source?
-Erythrocytes
-Retina
-Renal Medulla
-Brain.
-All cancer cells
What are two polysaccharides?
Cellulose and glycogen
What are two polysaccharides?
Cellulose and glycogen
What are the four fates of glucose?
- Undergoes oxidation through aerobic glycolysis to become pyruvate.
- Fermentation by anaerobic glycolysis to become lactate
- Undergoes oxidation through the pentose phosphate pathway to become Ribose-5-phosphate.
- To become Glycogen, Starch and Sucrose, for conversion of lipids.
How do glucose transport into cells?
Via Na+/glucose symporters
Via passive facilitated diffusion glucose transporters.
What are all the glucose transporters?
GLUT 1
GLUT 2
GLUT 3
GLUT 4
GLUT 5
Where can each GLUT be found?
GLUT 1- Brain
GLUT 2- Liver and B-cells
GLUT 3- Brain
GLUT 4- Muscle and adipose tissue
GLUT 5- Gut
What do Beta cells do?
Cells that make insulin, a hormone that controls the level of glucose (a type of sugar) in the blood.
What does KM stand for in biochemistry?
The Michaelis constant (KM) is defined as the substrate concentration at which the reaction rate is half its maximum value.
What glucose transporters have high and low KM?
Low KM: GLUT 1 and GLUT 3
High KM: GLUT 2
What are glucose transporters and insulin-dependent/independent fructose transport?
Insulin independent: GLUT 2
Insulin-dependent: GLUT 4
Fructose transport: GLUT 5
What is GLUT 1, and how does it function?
GLUT 1 is a glucose transporter.
Glucose binds to the outside active site and triggers a conformational change. The binding site faces inwards. Glucose is released into the cytosol. Conformational change regenerates the binding site on the outside.
What is glycolysis?
A linear metabolic pathway of enzyme-catalyzed reactions that converts glucose into two molecules of pyruvate in the presence of oxygen or two molecules of lactate in the absence of oxygen.
What is the overall reaction of aerobic glycolysis?
glucose + 2 ADP + 2 Pi + 2 NAD+
(Arrow)
2 pyruvate + 4 ATP +2 H2O + 2 NADH + 2 H+
What do you need to do to glucose to break it down?
Destabilize it because glucose itself is a very stable molecule.
What is the overall design of the aerobic glycolysis pathway?
Check-in notion
What happens in the three stages of glycolysis?
Stage 1: glucose is trapped and destabilized
Stage 2: two interconvertible three-carbon molecules are formed
Stage 3: generation of ATP
What are the two major cellular needs?
-Production of ATP
-Provision of building blocks for synthetic reactions
What are the control points in glycolysis, their names, and their functions?
-These are enzymes catalyzing irreversible reactions
1. Hexokinase – Substrate entry
2. Phosphofructokinase – Rate of flow
3. Pyruvate Kinase – Product exit
What are the three Irreversible/controlled reactions in glycolysis?
Hexokinase
-glucose + ATP –> glucose 6-phosphate + ADP + H+
Phosphofructokinase
-fructose 6-phosphate + ATP –> fructose 1,6-bisphosphate + ADP + H+
-Pyruvate kinase
phosphoenolpyruvate + ADP + H+–> pyruvate + ATP
Why is phosphofructokinase so important?
Key enzyme controlling the rate of substrate movement along the glycolytic pathway.
What are the two activators of glycolysis and their effect?
AMP and fructose 2,6-biphosphate.
-Will increase glycolysis if energy is needed.
What are the three inhibitors of glycolysis and their effect?
- ATP- Will slow glycolysis if energy is abundant
- Citrate - TCA cycle intermediate. Slows down downstream pyruvate entry to the TCA cycle if energy is abundant.
- H+ - Slows glycolysis if too much lactic acid is being produced
What does PFK stand for?
Phosphofructokinase
What is the ATP/AMP ratio called?
The energy ratio
When is a cell fully charged?
When all adenylate nucleotides are in the shape of ATP
When is a cell discharged?
When the cell only contains AMP and Pi
Why is AMP and not ADP the positive regulator? Use the formulae.
Because if ADP is rapidly used up, adenylate kinase can salvage some of the energy in ADP.
The formulae:
-ATP —> ADP + Pi
-2 ADP –> ATP + AMP
What is the fate of pyruvate?
Carbon to fuel the Citric Acid Cycle in mitochondria.
What is the fate of 2 NAD+ and 2 NADH + 2 H+
Electron transport chain and ATP synthesis
What two things happen if mitochondria metabolism is inhibited by lack of oxygen?
Anaerobic (Lactic and fermentation).
-NADH is used to ferment pyruvate to lactic acid (lactate)
-NADH is re-generated at the beginning of stage 3
Draw the intracellular stages of metabolism involving Glucose, Fatty Acids, and Amino Acids.
Check-in notion.
What is the Warburg Effect?
Up-regulation of anaerobic glycolysis in cancer cells
What do cancer cells do regarding the Warburg Effect?
Cancer cells produce energy by the high rate of glucose
metabolism to lactate (anaerobic glycolysis)
(That is why PET scans are used!)
Do cancer cells have Low or High KM Hexokinase?
Cancer cells have low KM Hexokinase
What are the four advantages of the Warburg Effect?
-Rapid energy production
-Supports other pathways for nucleotide synthesis (needed for growth)
-Supports rapid cell growth (proliferation)
What are the four disadvantages of the Warburg Effect?
-Produces H+ and lactate as end products
-Very inefficient ATP synthesis
-High glucose consumption demand
-Cancer patients lose weight
How do you treat cancer regarding the pathways in biochemistry?
You target glycolysis.
What three inhibitors are used to treat cancers, and where?
- 2-Deoxy-glucose: Competitive inhibitor. Blocks further
metabolism of G6P - 3-Bromopyruvate: Competitive inhibitor. Blocks production
of 1,3 bisphosphoglycerate - Dichloroacetate: Promotes conversion of lactic acid to pyruvate. By re-engaging mitochondrial metabolism, it slows the glycolytic rate. Cells can no longer sustain nucleotide synthesis and so cannot grow.
What is NAD+ derived from?
Niacin, a vitamin
What does glycolysis do to NAD+?
It reduces it to NADH + H+
NADH must be re-oxidized to let glycolysis stop; true or false?
False, to continue
How is NAD+ regenerated?
Through the oxidative metabolism of pyruvate
What does NADH deliver?
Delivers electrons to the respiratory chain
NAD+ is regenerated as what and why?
NAD+ is re-generated as an electron acceptor to maintain
Stage 1 and Stage 2 metabolism
What are the two other names for the Citric acid cycle?
- Krebs Cycle – Sir Hans Krebs
- Tricarboxylic acid (TCA) cycle – Because some molecules have 3 carboxyl groups.
Where does the TCA cycle occur?
In the mitochondria.
What two elements are essential for the TCA cycle and why?
- Inner membrane: Contains proteins for electron transport chain, ATP synthase, and transport proteins.
- Matrix: Contains enzymes of the TCA cycle.
How does pyruvate enter the mitochondrial matrix? Tell me the three steps.
-H+ gradient from the cytosol to matrix
-Pyruvate transporter: H+/pyruvate symport by facilitated diffusion.
-A similar process regulates ADP, ATP & inorganic phosphate (Pi) movement into and out of mitochondria.
Once in the matrix, how is pyruvate metabolized to Acetyl-CoA?
The pyruvate dehydrogenase complex (PDC) catalyses the oxidative decarboxylation of pyruvate to acetyl-CoA
What does the Pyruvate dehydrogenase complex consist of, and what is it regulated by?
It consists of 3 enzymes and is allosterically regulated by phosphorylation.
What does PDC activity determine?
Glucose oxidation in well-oxygenated tissues
Is PDC activity reversible?
The reaction is irreversible. Acetyl-CoA cannot be converted
back to pyruvate.
Tell me the four steps of how pyruvate becomes Acetyl CoA-
- Pyruvate loses CO2 and Hydroxyethyl TPP (HETPP) is formed.
- Hydroxyethyl group is transferred to lipoic acid and oxidized to form acetyl dihydrolipoamide.
- Acetyl group is transferred to CoA
- Dihydrolipoamide is reoxidized
What are the three enzymes in the four stages of PDC?
Stage 1: Pyruvate dehydrogenase
Stage 2 & 3: Dihydrolopoyl transacetylase
Stage 4: Dihydrolipoyl dehydrogenase
How many reactions are there in the TCA cycle?
Eight reactions in total.
Draw the TCA
Check-in notion
Where are all enzymes of the TCA cycle located? Except for what enzyme?
In the mitochondrial matrix
Succinate dehydrogenase, which is integrated into the inner mitochondrial membrane.
What are the three control mechanisms in the TCA cycle?
- High ATP, NADH, and acetyl-CoA means plenty of energy
- High ADP and NAD+ mean lack of energy
- High succinyl-CoA and acetyl-CoA means plenty of precursor molecules for biosynthetic reactions
Describe the links between glycolysis, the TCA cycle, and oxidative phosphorylation (Lee más en esto)
The connecting link between glycolysis and the TCA cycle is Acetyl CoA.
Glycolysis is the first step of cellular respiration and is common to aerobic and anaerobic organisms because it occurs without oxygen. The product of glycolysis is pyruvate which is oxidized to acetyl-CoA, and it is acetyl-CoA that enters mitochondria and takes part in the Krebs cycle. There is the release of carbon dioxide; thus, the process is known as decarboxylation. There is acetate formation, which binds with CoA to form acetyl-CoA. NAD molecule is reduced to form NADH. It takes place in the presence of the enzyme pyruvate dehydrogenase. This reaction is the connecting link between glycolysis and the Krebs cycle.
What is an example of Stage II Metabolic disorder, and explain it: What is it, the genes, the carrier, and how does the offspring react?
Pyruvate Dehydrogenase Complex Deficiency.
Pyruvate Dehydrogenase (PDH) is an enzyme of the pyruvate
dehydrogenase complex.
Its gene is located on the X chromosome, therefore carrier: X
There are four options for offspring:
1. XX and XY: unaffected
2. XX (One affected gene): Survivable, adolescent Onset, and variable symptom severity.
3. XY (One affected gene): Lethal, stillborn
How does PDC deficiency present, what symptoms does it cause, and what can you see in the imaging?
-It presents mainly as a neurological disease in children.
-Symptoms: hypotonia & lack of coordination, retardation & seizures, persistent lactic acidosis, and respiratory problems.
-In imaging, you can see Brain lesions and defective symmetry of the left and right hemispheres.
Overall how many NADH + H+ and FADH2 are produced from one glucose molecule, the reactions of glycolysis, pyruvate dehydrogenase complex, and the TCA cycle? And what does each one of them carry?
10 NADH + 10 H+
2 FADH2
-They carry two HIGH-ENERGY electrons
What is oxidative phosphorylation?
The process by which electrons move down an electron transport chain, resulting in the formation of ATP from ADP
Where does oxidative phosphorylation occur?
In the mitochondrion
What are electrons from NADH and FADH2 used for? And what is the function of their energy?
Used to reduce O2 to H2O
Their energy is used to pump protons (H+) from the mitochondrial matrix to the intermembrane space
pH decreases in intermembrane space, increases in the matrix
True or false?
True!
Why do protons flow back across the membrane?
They are following their concentration gradient.
What energy is used to phosphorylate ADP to ATP?
The energy of proton flow
When is 2 NADH formed, and where?
During glycolysis in the cytoplasm.
What is the Electron transport chain?
The ETC is a collection of proteins bound to the inner mitochondrial membrane and organic molecules, which electrons pass through in a series of redox reactions and release energy.
Can NADH cross the inner mitochondrial membrane? Can it be re-oxidized to NAD+ directly using the electron transport chain
Nope and nope
How does the NADH from the cytoplasm get into the mitochondrion?
The glycerol-3-phosphate and malate-aspartate shuttles
What are the three steps of the Malate-Aspartate Shuttle? (You can write or do the sketch)
- NADH from glycolysis is used to generate malate from oxaloacetate in cytosol
- Malate transporters transfer malate to the mitochondrial matrix.
- Malate conversion to oxaloacetate in the TCA cycle generates NADH in addition to the malate that arises from Fumarate.
What is phosphoryl transfer potential?
The standard free energy of hydrolysis—is a means of comparing the tendency of organic molecules to transfer a phosphoryl group (PO3) to an acceptor molecule.
What is electron transfer potential?
Based on the difference in the affinity of elements/molecules to bind electrons. Moving one electron from one place to another.
How can phosphoryl and electron transfer potential be measured?
Phosphoryl transfer potential can be measured by the free energy change, DGo’, for the hydrolysis of ATP.
Electron transfer potential is measured by the redox potential (or reduction potential), E’o, of a compound.
In oxidative phosphorylation, the electron transfer potential of NADH+ and FADH2 is converted into…
The phosphoryl transfer potential.
What is the standard redox potential of a reduced substance?
The standard redox potential E’o of a (reduced) substance X is a measure of how readily X donates an electron (in comparison with H2)
X- –> X + e-
What does a negative and a positive E’o mean?
That the reduced form of X has a lower affinity for electrons than H2, a positive E’o means the opposite
The standard free energy change is proportional to…
The change in standard redox potential and the number of electrons transferred
What is the driving force of oxidative phosphorylation?
Energy released by the reduction of O2 by NADH
What is the standard free energy change for the hydrolysis of ATP?
31.4 kJ/mol
How is the energy of the electrons converted into the energy of ATP?
The energy released in the electron transport chain is captured as a proton gradient, which powers the production of ATP by a membrane protein called ATP synthase.
What is chemiosmosis?
Chemiosmosis is the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient.
What two stages does Oxidative phosphorylation consists of, and what do they involve?
- Electron transport: electrons flow from NADH and FADH2 to O2, respiratory chain and energy is used to pump H+ out of the mitochondrial matrix
- ATP synthesis: electrochemical gradient of H+ across the mitochondrial inner membrane, and the energy stored in this gradient can be used to synthesize ATP.
What do separate proton pumps catalyze?
Electron transport and ATP synthesis
What are the four complexes + 1 stage in the respiratory chain?
- Redox of NADH + H+ at complex I, electrons go to Complex I, and four protons are pumped from the matrix to intermembrane space.
- Redox of FADH2 at Complex II, coenzyme Q picks up electrons (From complex I and II) and transports them to Complex III
- Redox of Complex III, four protons pumped from matrix to intermembrane space, carrier C transports electrons to Complex IV.
- Redox of Complex IV, two protons pumped from matrix to intermembrane space, formation of H2O (20% of water in the body)
-ATP synthase action pumps protons from intermembrane space to matrix and produces ATP from ADP + Pi + energy.
What is Complex II part of?
The TCA cycle!
What are two characteristics of Q (Coenzyme Q (Ubiquinone))
-Hydrophobic
-Shuttles rapidly within the membrane
Is cytochrome C soluble?
Yes
Draw the diagram of the respiratory chain.
Check-in notion
What are cytochromes?
Cytochromes are proteins that contain a haem group as a functional co-factor
What does Haem contain, and what can that do?
Haem contains a Fe(II) ion which can take up and release electrons
What is the H+ Pump, and what complexes pump H+?
Pump hydrogen ions across the mitochondrial inner membrane from the matrix into the intermembrane space.
Three of the four respiratory complexes pump H+
What is the electrochemical gradient?
The electrochemical gradient measures the free energy available to carry out the useful work of transporting the molecule across the membrane.
Where can you find the most protons, intermembrane space or matrix?
Intermembrane space
What two separate ways do protons flow?
The respiratory chain pumps protons into intermembrane space
Protons flow back through ATP synthase
What two structures does the ATP synthase has and where are they located?
F0: Elongated– F0 subunit is a hydrophobic complex in the inner membrane
F1: Circular– F1 subunit protrudes into the mitochondrial matrix
What is the ATP synthase also called?
-Mitochondrial ATPase
-F1F0ATPase
What does the F0 Subunit contain?
Contains a proton channel
What subunits form the stator?
a, b, alpha, beta, and delta subunits
What subunits form the rotor?
c, gamma, and epsilon subunits
What does the proton flow do, and what does this lead to?
The flow of protons turns the rotor.
This conformational changes lead to ATP synthesis.
What five ways can you inhibit Oxidative Phosphorylation?
- Rotenone and amytal
- Antimycin A
- Myxothiazol
- UHDBT
- Cyanide, azide and carbon monoxide
What can cyanide, azide, and carbon monoxide do?
Inhibit transfer of electrons to O2, so no proton gradient can be formed, and no ATP can be synthesized.
What is non-shivering thermogenesis?
An increase in metabolic heat production (above the basal metabolism) that is not associated with muscle activity
In what three organisms does non-shivering thermogenesis maintain body temperature?
hibernating animals
newborn animals (incl. human)
cold-adapted mammals
What does brown adipose tissue contain and generates?
Uncoupling protein (UCP) = “thermogenin”
It generates heat by short-circuiting the mitochondrial battery
What is the P/O ratio?
A measurement of the coupling of ATP synthesis to the electron transport, the number of molecules of inorganic phosphate (Pi) incorporated into ATP per atom of oxygen used
What does the P/O ratio depend on?
Depends on the substrate which is oxidized
if NADH is oxidized to NAD+
P/O ratio = 2.5
if FADH2 is oxidized to FAD
P/O ratio = 1.5
What does the P/O ratio demonstrate?
Demonstrates the complexity of oxidative phosphorylation is strongly influenced by Uncoupling Protein Activity.
How much ATP does one glucose molecule yield?
30 to 32 ATP molecules
