Chapter 3 - Biochemical Pathways Flashcards
Active Site
Particular region of an enzyme into which the substrate fits: pocket or groove formed by folding of the polypeptide chain (tertiary structure of the protein
Anabolic Reaction
A reaction that builds up complex molecules from more simple ones
Enzyme-substrate Complex
The step where a substrate binds to an active site of an enzyme forms the enzyme-substrate complex
Substrate
The substance binding to an enzyme to be catalysed
Function of enzymes and purpose.
Substrate binds to an enzyme at an active site, and the enzyme changes shape to fit around the molecule forming enzyme - substrate complex . The bonds of the substrate are stretched and weakened by molecular interactions between the substrate and enzyme. Thus a lower energy pathway is required for the reaction to occur. A lower activation energy is required for the reaction therefore reaction proceeds at required rate.
Co - factors and Co-enzymes
Co-factors are non protein compound that activate the action of an enzyme. Co-enzymes are a type of co-factor but are limited to organic co-factors only. Non Co-enzyme cofactors: Inorganic metal ions permanently bound to active site
CoEnzymes:
organic
non-protein
loosely bound to active site
Globular VS Fibrous Protein
Globular: Eg.) Egg, casein
folded ball like structures
soluble
have comparatively weak intermolecular forces
Fibrous: Eg.) Silk, skin, wool
Thin, thread like structure
insoluble
If energy is lost in a biochemical reaction it is….
Exergonic: releases energy
catabolic: breakdown of compounds complex–>simple
If energy is absorbed in a biochemical reaction it is….
Endergonic: requires energy
Anabolic: simple —>complex molecules
Protein denaturation, cause and concqeunce
Caused by..
High temperature: breaks bonds and disrupts tertiary structure
pH; Too much H+ or OH- interacts with bonds and changes 3D shape.
Protein can no longer function as required.
Metal ions: Charge disrupts bonds between amino acids.
detergents and solvents: For bonds with non-polar groups thus causing hydrogen bonding
Increase rate of reaction by:
Increase enzyme concentration,
increase temp
decrease product concentration
increase substrate concentration
Note: All changes have a saturation point where further increases either have no impact or a detrimental one.
two types of inhibition:
Non-competitive:
Substance binds to enzyme, not at the active site and changes the shape of the enzymes active site so it cannot bind with substrate.
Competitive enzyme:
binds to the active site of the enzyme, inhibiting the substrate from binding to the active site.
anaerobic glycolysis inputs and outputs
Glucose + NAD + H+ +2ADP +2pi—> 2*Pyruvate + NADH + 2ATP
What cells use cellular respiration?
All living organisms respire as it is required for growth, however some organism cannot respire aerobically (mostly bacteria).
Alcohol fermentation
- What organisms
- inputs and outputs
plants, fungi, bacteria
2* Pyruvate —–> Ethanol + 2*CO2
lactic acid fermentation
- What organisms
- inputs and outputs
Animals
2* Pyruvate —–>Lactic acid
Krebs Cycle inputs & Ouputs:
don’t need to know numbers
Inputs: 2 Acetyl CoA, 2 (ADP+Pi), 8 (NAD+ +H+), 2 FAD, 6 O2
Outputs: 2ATP, 6 CO2, 8 NADH, 2 FADH2
Electron transport chain Inputs and Ouputs
Inputs; 32 (ADP+pi), 10 NADH, 2 FAD, 6 O2
Outputs: 32 ATP, 10 NAD+, 10 FAD, 6 H20
Balanced Photosynthesis equation
6CO2+12H20 ——Energy—–>C6H12O6 + 602 + 6H2O
Photosynthesis Light dependant inputs & outputs
Inputs: Light, H2O, NADP+, ADP+Pi
Outputs: 6 O2 + NADPH +ATP
Photosynthesis Light independant inputs & outputs
Inputs: 6 CO2 + ATP + NADPH
Outputs: Glucose, H20, ADP+p1, NADP+
Hydrogen ion carriers for photosynthesis and respiration
Photosynthesis: NADP+ —>NADPH
Respiration: NAD—NADH
FAD–FADH2
Location of light dependant phase of photosynthesis:
Thylakoid membrane.
Ganum
Stack of thylakoid disks inside a chloroplast
Location of light independant phase of photosynthesis:
stroma (aqueous space)
Factors effecting photosynthesis
Co2, O2, H20, chlorophyl levels
Light intensity
temp
Why are some plants not green
Plants contain other photopigments which absorb different wavelengths of light.
however all plants contain chlorophyl as it is required for photosynthesis to occur.
Key steps light dependant phase of photosynthesis
1.) Chlorophyl absorbs light and uses the energy to split H20 into 2 H+, 1/2 O2 and 2 e-.
2,) Energy from electrons used to pump H+ across thylakoid membrane
2,) H+ gradient is created and is used to synthesis ATP in ATP synthase. NADPH also forms at the end of the chain
Light dependant phase Summary:
- Occurs at Thykaloid membrane
- Chloroplast pigment absorbs light, excite electrons and enable H2O to split.
- Energised electrons move across membrane through proteins and pump hydrogen ions into thykaloid. - Concentration gradient of H+ is established, its potential energy used to synthesise ATP.
- The electrons are accepted by a NADP+ molecule allowing a H+ to bind to form NADPH.
Light independant phase Summary:
- Occurs in the Stroma.
- 3 Carbons from CO2 bind to carbon chain molecule. This is known as carbon fixation and occurs in the presence of the enzyme Rubsico.
- Series of chemical reactions which require ATP and NADPH break down carbon chain.
- 3 carbon G3P leaves the cycle and is used to create glycogen or other carbohydrate structures.
- Cycle continues as long as there is sufficient CO2, ATP, NADPH and enzymes.
Glycolysis Summary:
6 carbon glucose molecule splits into 2 pyruvate molecules providing the energy for for 2 ATP and NADH to be synthesised.
Krebs Cycle Summary:
- No oxygen required, occurs in mitochondrial matrix
- Pyruvate is broken down into Acetyl-CoA releasing one CO2.
- Acetyl-CoA is added to carbon chain and is subject to a series of chemical reactions which release CO2 in the process.
- During the cycle chemical reactions provide energy for the synthesis of 2 ATP and multiple NADH & FADH2 molecules.
Electron transport chain Summary
excited electrons from NAD + H+ split is transported across cristae membrane, providing energy for H+ to be pumped against its concentration gradient.
- The potential energy from the H+ concentration gradient provide energy for the synthesis of ATP.
What is rational drug design?
Refers to the production of drugs that are specifically designed in terms of three dimensional shape and structure as to specifically interact with target molecules and proteins
Compartmentalisation & feedback inhibition in relation to chemical reaction pathways
Compartmentalisation: specific membrane bound organelles allow for ideal chemical environment for reaction and insure all required enzymes and chemicals required are in one place.
feedback inhibition: too many products decreases rate of chemical reaction
