BIOSCI 101 BioChem Short Answers Flashcards
What are the 2 Laws of Thermodynamics?
Energy is conserved, the Universe is becoming more disordered.
Which Food Sources Release which amounts of Energy when Combusted?
Least to most: carbohydrates, proteins, alcohol, fat.
How many Kcal/g are in Carbohydrates, Proteins, Fats and Alcohol?
Carbohydrate: 4
Protein: 4
Fat: 9
Alcohol: 7
What is the Main Contributor to Useful Energy per Oxygen?
Access to C-C bonds.
Which Food Sources Give which amounts of Energy per Oxygen?
Least to most: fat, alcohol, protein, carbohydrate.
How does ATP Work?
Negative charges repel each other, making ATP unstable - making molecular spring to force reactions, shape/charge changes.
What is Unique about the Energy Released from ATP?
Energy released from the terminal phosphate of anhydride bond hydrolysis, is high.
What happens to the Free Energy of Formation of ATP?
IT is greater than the sum of the products of formation of ADP + Pi.
How do you Calculate G?
H - T S = G
Energy of reaction - Change in order = Change in energy for a given reaction
What is the 1st Law of Thermodynamics?
H = q + w Enthalpy = Heat + work done
What is the 2nd Law of Thermodynamics?
Systems will progress towards increased entropy.
What is Entropy?
Symbol S. Turning in - a measure of order.
What is G?
Gibbs free energy.
How does an Exothermic Reaction relate to H?
Has a negative H by convention - the enthalpy of the products is lower than the reactants.
How can we Understand Glycolysis Simply?
It is sugar splitting - glyco-lysis.
Which Bonds are Oxidised in Biology?
C-H bonds.
What are the 2 Main Reaction Types in Metabolism of Fuels?
Rearrangement/Preparation
Oxidation/Reduction
What are the 3 Types of Oxidation?
Alcohol to ketone, alkane to alkene, aldehyde to an acid.
Which Enzyme is Responsible for Biological Redox Reactions?
Dehydrogenases.
What is Involved in all Oxidation Reactions?
Hydrogen.
What is LEOGER?
LEO refers to the loss of an electron (oxidation), GER refers to the gain of an electron (reduction).
Why can only C-H Bonds be used in Oxidation?
Lipids in membranes; full of C-C bonds, oxidising these would metabolise our membranes, C-C bonds form backbones of sugars.
What are the 3 Stages of Cellular Respiration?
Glycolysis, citric acid cycle, oxidative phosphorylation.
What is Important to Remember about Km and Affinity?
Km is the reciprocal of affinity.
What Happens in the Trapping and Investment Stage of Glycolysis?
Glucose is trapped in the cell, phosphate charged and glucose not recognised by GLUT, Glucose-6-Phosphate tagged for other things.
What Happens in the 1st Rearrangement Stage in Glycolysis?
Phosphoglucoisomerase catalyses rearrangement of glucose-6-phosphate to fructose-6-phosphate.
What Happens in the Commitment and Investment Stage of Glycolysis?
Phosphofructokinase converts ATP to ADP, adding a phosphate to fructose-6-phosphate, forming fructose-6-biphosphate.
What Happens in the 2nd Rearrangement Stage in Glycolysis?
Aldolase splits fructose-6-biphosphate into dihydroxyacetonephosphate and glyceraldehyde-3-phosphate.
What Happens in the Oxidation (Energy Harvest) Stage in Glycolysis?
There is an injection of Pi, using no ATP - a phosphate is added.
What Happens in the 2nd Energy Harvest Stage in Glycolysis?
Phosphoglycerokinase turns 2 ADP into 2 ATP, removing a P.
What Happens in the 3rd Rearrangement Stage in Glycolysis?
Phosphoclyceromutase moves a phosphate up to carbon chain.
What Happens in the 4th Rearrangement/Dehydration Stage in Glycolysis?
Enolase removes 2 H2O to form a pyruvate.
What Happens in the Final Energy Harvest Stage in Glycolysis?
Pyruvate kinase turns 2 ADP into 2 ATP, forming pyruvate.
What are the ATP Yields at each Phase of Glycolysis?
Investment - 2 ATP
Payoff - 4 ATP
Net gain of 2 ATP
How is ATP Captured in Glycolysis?
By substrate level phosphorylation.
What is Important to Remember about Glycolysis?
It is highly regulated and irreversible in vivo.
What are the 4 Regulators for PFK?
Inhibited by high ATP, AMP activates PFK, also inhibited by citrate from the CAC, proton numbers inhibit PFK.
What is NAD Reduced to?
NADH.
What Happens to Glycolysis if there is no Oxygen?
There is limited NAD in cells so it stops - must be regenerated by lactate.
Which 2 Factors Lead Kreb to Discover the CAC?
Citrate did not vanish, pyruvate had 1 too many carbons.
What Discovery did Kreb Make that Linked Glycolysis to Respiration?
There was a loss of C from pyruvate to make acetate, which leads to making citrate.
What does Glucose Produce in the Citric Acid Cycle?
6CO2, 8NADH + H, 2FADH2, 2GTP (or ATP).
What does Glucose Produce in Glycolysis?
2NADH and 2ATP.
How does Pyruvate Lead to Acetyl CoA?
Pyruvate is decarboxylated then oxidised and then CoA attached.
What Happens in Stage 1 of the Citric Acid Cycle?
Acetyl group adds 2C to oxaloacetate.
What is Unique about Aconitase?
It has an iron-sulphur complex; very sensitive to free radical superoxide and damaged in diseased states.
What Happens in Stage 2 of the Citric Acid Cycle?
H2O removed and re-added - rearrangement.
What is Isocitrate Dehydrogenase?
A regulator enzyme, increases activity with Ca and decrease with high ATP/ADP ratios.
What Happens in Stage 3 of the Citric Acid Cycle?
NAD is reduced to NADH and CO2 is removed.
What Happens in Stage 4 of the Citric Acid Cycle?
Another CO2 removed and another NAD reduction, and CoA-AH added (weak bond).
What Happens in Stage 5 of the Citric Acid Cycle?
CoA-SH released and substrate level phosphorylation, GTP formed and converted to ATP at no cost.
What Happens in Stage 6 of the Citric Acid Cycle?
2 H transferred to FAD (FADH2), succinate oxidised.
What is SDH?
Part of the electron transport system - in the inner mitochondrial membrane.
What is the Role of SDH?
Handles some very dangerous free radicals, but appears very robust.
What Happens in Stage 7 of the Citric Acid Cycle?
Water added to fumarate and rearrangement.
What Happens in Stage 8 of the Citric Acid Cycle?
Last oxidation and oxaloacetate reformed.
How how Stages of Oxidation are there in the Citric Acid Cycle?
4.
What is ESSENTIAL to Remember about the Citric Acid Cycle?
Glucose makes 2 pyruvates, so there are basically 2 CACs occuring simultaneously.
What are the 2 Regulators of Metabolism and the CAC?
ATP/ADP and NADH.
What Effect does High NADH Have?
A lot of reducing power.
Which Ratio is also Known as the Redox State?
NADH/NAD ratio.
How is IDH Activity Regulated?
ADP/ATP ratio:
10/2 goes faster
2/10 goes slower
Also Ca
What Impact do Large Quantities of Succinyl/Acetyl-CoA Have?
CoA becomes limiting and the CAC slows.
What are the 2 Benefits of Mitochondrial Fusion?
Enhanced ATP production, protects mitochondria from degradation.
What is the Redox Potential for NADH in ETS?
1.135V.
What is the Redox Potential for FADH2 in ETS?
0.815V.
How do Electrons Flow through Iron Sulphur Clusters?
The Fe atoms change oxidation state (Fe3 to Fe2), and act as a wire to ‘conduct’ electrons.
What is Ubiquinone?
Oxidised form of Coenzyme Q.
What is Semiquinone?
1/2 reduced/oxidised form of Coenzyme Q.
What is Ubiquinol?
Reduced form of Coenzyme Q - two alcohols.
Which Factors can Impact Complex 1?
Anaesthetics - rotenone, amytal.
Which Factors can Impact Complex 2?
Mythioxiol, antimycin a.
Which Factors can Impact Complex 4?
Cyanide, nitric oxide, CO, H2S.
How many Protons are Shifted for 1 NADH + H?
10 protons.
Which Complexes Transfer Protons in ETS?
Complexes 1, 3, 4.
How many more Hydrogens does NADH move than FADH2?
4 more hydrogens.
How are Oxidation and ATP Synthesis Coupled?
By transmembrane proton fluxes.
What Happens to the Excess Protons from the Proton Fluxes?
A chemiosmotic gradient forms.
What is Unique about the Gradients within Mitochondria?
There is a chemiosmotic gradient - both and electric potential and chemical gradient.
What Addition enabled ATP Synthase to make ATP?
The addition of OH.
What are the 2 Major ways to Stop ATP Synthesis?
Chemicals can uncouple the proton gradient or poison the electron flow.
How do Proton Gradients Lead to Photosynthesis?
Electron flow drives proton pumps, protons accumulate in gradients, protons then drive ATP synthesis.
What are the 2 Components of the Proton Motive Force?
Concentration gradient and an electric charge.
What is the Average pH of the Mitochondrial Matrix and the Inter-membrane Space?
Matrix: 7.8
IMS: 7.6
How is it Ensured that the Protons don’t diffuse Randomly in the Bulk Stage?
Phosphate heads of lipids are -vely charged and H is attracted to these heads, so flow along the membrane, separated by thin water layer.
How is Cristae Shape Determined?
The dimerised ATP synthases fold the inner membrane to give their shape.
Where is the Greatest Negative Charge on Cristae?
Inside surface tips.
How do Cristae Enable ATP Synthase to be Driven?
Protons gathered around inside surface tips lower local pH to 6.
What does Organisation of OXPHOS Achieve?
Enhances proton flow, concentrates the effort.
What is Important to Remember about the Internal Rod in the ATP Synthase Machine?
It isn’t straight.
What Happens to the ATP Synthase Rotor if ATP is added?
It can spin backwards and act as a proton pump.
How many ATP are Made for Each Rotation of the Internal Rod in ATP Synthase?
3 ATP.
How can we Judge the Number of ATP Made based on C Ring Size?
The bigger the C ring, the less ATP is made per proton.
What are the 2 Ways of Using the NADH Formed in Glycolysis?
Malate Aspartate shuttle, G3PDH shuttle.
Why is the Yield of ATP Vague?
Membranes leak when hot, NADH from glycolysis has 2 fates.
Which Shuttle Produces More ATP - Malate Aspartate or G3PDH?
Malate Aspartate.
Which Complex is Most Impacted by Damage?
Complex 1: oxidative stress, heart attack etc.
What Happens if Inner Mitochondrial Membranes become Damaged?
Uncoupling proteins are activated (ACPs), increasing leakiness.
Which 2 Tissues Release Glucose?
Liver and kidneys.
How does Glycogen Protect Osmotic Pressure of a Cell?
Small glucose molecule attracts water, large polymers do not.
What is Glycogen?
Storage of glucose in the cytosol.
Why can Muscle hold Less Glycogen than the Liver?
Space limits.
Which Bond in Glycogen is Branching?
Alpha 6.
What is Glycogenesis?
Glycogen birth.
How is Glucose Trapped in the Hepatocyte?
Phosphorylation - charge is changed.
What does Glucose Pass Through to Enter the Hepatocyte?
A GLUT.
How is UDPG Formed?
G1P + UTP - energy has been invested.
Where is Glucose Added?
Non-reducing ends.
How can we Remember the Difference Between Alpha 4 and Alpha 6 Bonds?
Alpha 6 branch off - like workers to the pub at 6.
How is Glycogen made Dense?
Branching enzyme creates new branches towards the core.
What is Glycogenolysis?
Glycogen cutting/breakdown.
Where is Glycogen Broken Down?
From the non-reducing ends - other end is buried in glycogen mass.
How does Glycogenolysis Work?
G1P is released - working to leave 4 glycosyl residues.
Why is Hydrolysis not Used to Break Down Glycogen?
Hydrolysis leaves an unphosphorylated glucose, released glucose is chraged and trapped in cells, saves an ATP as Pi is used.
Where is G6Pase Found?
Only in the liver and kidneys.
What does Coordinated Control of Glycogen Metabolism Ensure?
Glycogen is not being made as it is broken down.
What is von Gierke’s Disease?
Mutation in G6P, can’t release glucose from liver.
What is Mc Ardle’s Disease?
Lack of glucose release, so little glycogen phosphorylase activity in muscles (cramp).
What is Gluconeogenesis?
Making glucose.
What are the Building Blocks of Gluconeogenesis?
Lactate, amino acids, glycerol, TCA intermediates.
Which 3 Reactants of Gluconeogenesis are Important to Remember?
4ATP, 2GTP, 2NADH.
When are Glycolysis Reactions Reversible?
When the reactants and products are in equilibrium.
Which 3 Bypasses are required for the Kinases?
Bypass 1, 2 and 3.
Which Enzymes are Used in Bypass 1?
Pyruvate carboxylase, PEPCK.
Which Enzymes are Used in Bypass 2?
Fructose 1,6-biphosphatase.
Where does Bypass 1 Take Place?
Cytosol and mitochondria.
Where does Bypass 2 Take Place?
ER, cytosol.
Which Enzyme is Used in Bypass 3?
Glucose 6-phosphatase.
What is the Balance of ATP Between Gluconeogenesis and Glycolysis that Proves they Shouldn’t Run Together?
Gluconeogenesis consumes 12 ATP, glycolysis makes 2 ATP, mis-match of -10 ATP.
Which Endocrine Organ Maintains Glucose Levels?
The pancreas.
What do the Endocrine Islets of Langerhans do?
Secrete hormones.
What do Exocrine Glands in the Pancreas do?
Secretes digestive enzymes.
When do Alpha Cells Produce Glucagon?
When there is low blood glucose.
How does Glucagon Raise Blood Glucose Levels?
Stimulates glycogen breakdown, signals liver cells to turn glycogen into glucose for the blood.
When do Beta Cells Produce Insulin?
When there is high blood glucose levels.
How does Insulin Lower Blood Glucose Levels?
Stimulates all body cells to take up glucose (except brain).
What are the 2 Other Effects of Insulin?
Stimulates glycogen synthesis, promotes storage of fuel.
What does Insulin do?
Drives glucose uptake in tissues, importantly the skeletal muscle and the liver.
Which Broad Hormone Family is Insulin Part of?
Anabolic.
Which 3 Things can Insulin Promote?
Fat deposition, glycogen storage, growth.
What are the Normal Levels of Blood Glucose?
4.5 - 5 mM.
What Happens to the Heart with Cardiomyopathy?
Heart muscle becomes enlarged.
What Happens to the Kidney due to Nephropathy?
Granular surface, decreased function, smaller size, high urine protein.
What is Diabetes?
Typically hyperglycaemic - excess glucose in blood appears in urine.
What are the Characteristics of Type 1 Diabetes?
Autoimmune disorder, usually appears in childhood - cannot produce insulin.
What is the Treatment for Type 1 Diabetes?
Insuline injections.
What are the Characteristics of Type 2 Diabetes?
Target cells have decreased responsiveness to insulin, 90% of Diabetes cases.
What Happens on the Cellular Level as a Result of Type 2 Diabetes?
Cells desensitised, beta cells work harder to supply large body mass and fail, uptake and disposal of glucose impaired.
What Happens when there is too much Fuel?
Too few mitochondria, they produce free radicals, cell protects itself by decreasing GLUTs, blood glucose rises.
What can Improve and Eradicate Type 2 Diabetes?
Exercise.
What Fuel Switch Occurs due to Starvation?
Glucose to ketone bodies used in the brain.
Where is Acetone Expired?
In the breath.
How does Ketone Used in the Brain Change due to Starvation?
3 days starvation - 30% ketones, 40 days - 70% ketones.
What is Ketoacidosis?
Where the pH of the blood drops due to use of ketone bodies rather than glucose.
How is ATP Replaced during Muscle Use?
By creatine phosphate almost immediately.
What Happens if ATP Stores Decline?
Cells die by necrosis.
Why do we Use Anaerobic Pathways?
Creatine phosphate and glycogen are self contained within cells, oxygen pathways have to wait for oxygen transport.
Where are Light Reactions Carried out?
In the thylakoid membranes.
What are the 2 Outcomes of Light Reactions?
Convert light to chemical energy of ATP and NADH, split H2O and release O2.
Where is the Lack of Absorbance of Chlorophyll?
Wavelength of 500 - 600 nm.
What is the Chemical Equation of Photosynthesis?
H2O + CO2 = (CH2O) + O2
What are Chloroplast Antennae Used for?
To acquire more electrons (100 photons per second).
How does Photosystem 2 Harvest Light?
Light hits PS2, electron jumps up, transferred to Q, goes to cytochrome complex, oxidises Q through Q cycle.
How does Photosystem 1 Harvest Light?
Light hits PS1, electron jumps up, 2 fates; electrons can move down string, NAD can be reduced to NADH.
Which Photosystem Comes First in the Chain of Linear Electron Flow?
Photosystem 2 - photosystem 1 was just discovered first.
How does the Cytochrome Complex Make ATP?
Indirectly - transferring 4 H+ - these drive ATP synthesis as in mitochondria.
What are the 2 Ways a Proton Gradient is Formed?
Splitting of water, cytochrome complex transfers 4 H+ to in thylakoid space.
How do C-Ring Subunits Compare between Plants and Mammals?
Plants have 14, mammals have 8.
What are the Differences between the Gradients of Mitochondria and Chloroplasts?
Mitochondria - uses proton gradient and electrical charge
Chloroplast - Proton gradient only
What are the Differences in Reduction between Mitochondria and Chloroplasts?
Mitochondria: es reduce oxygen
Chloroplasts: es reduce NADP
Why Have Cyclic Electron Flow?
Produces only ATP, some bacteria only have PS1.
What is the Cyclic Electron Flow?
Where the electrons take an alternate path - using PS1 but not PS2.
What is Pq in the Light Reactions?
Plastoquinone/ol.
What is Pc in the Light Reactions?
Plastocyanin.
Where does the Calvin Cycle Take Place?
The stroma.
What are the 3 Phases of the Calvin Cycle?
CO2 fixation, reduction, regeneration.
What is RuBisCo?
The most abundant protein on Earth.
What Happens to Carbon Numbers during Carbon Fixation in the Calvin Cycle?
3 x 5C becomes 6 x 3C.
How many Calvin Cycles are Required to make 1 Glucose?
2, with 1 G3P being removed each cycle.
What are the 2 Ways the Calvin Cycle is Regulated by Light?
pH, antioxidant enzyme.
How does pH Regulate the Calvin Cycle?
More alkaline the stroma, the faster the cycle works.
How does an Antioxidant Enzyme Regulate the Calvin Cycle?
Reduces RuBisCo.
Why is RuBisCo Useful?
Many plants shut down photosynthesis at midday - C4 plants store CO2 to survive hot climates.
What is the Purpose of the C4 Pathway?
C3 is wasteful, C4 concentrates CO2 so less O2 is present for photorespiration.
How does the C4 Pathway Accomodate for more ATP being Used?
Uses the cyclic electron flow.
