Chapter 3 - Biochemical Pathways

Question 1

Active Site

Answer 1

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

Question 2

Anabolic Reaction

Answer 2

A reaction that builds up complex molecules from more simple ones

Question 3

Enzyme-substrate Complex

Answer 3

The step where a substrate binds to an active site of an enzyme forms the enzyme-substrate complex

Question 4

Substrate

Answer 4

The substance binding to an enzyme to be catalysed

Question 5

Function of enzymes and purpose.

Answer 5

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.

Question 6

Co - factors and Co-enzymes

Answer 6

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

Question 7

Globular VS Fibrous Protein

Answer 7

Globular: Eg.) Egg, casein
folded ball like structures
soluble
have comparatively weak intermolecular forces

Fibrous: Eg.) Silk, skin, wool
Thin, thread like structure
insoluble

Question 8

If energy is lost in a biochemical reaction it is….

Answer 8

Exergonic: releases energy
catabolic: breakdown of compounds complex–>simple

Question 9

If energy is absorbed in a biochemical reaction it is….

Answer 9

Endergonic: requires energy
Anabolic: simple —>complex molecules

Question 10

Protein denaturation, cause and concqeunce

Answer 10

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

Question 11

Increase rate of reaction by:

Answer 11

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.

Question 12

two types of inhibition:

Answer 12

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.

Question 13

anaerobic glycolysis inputs and outputs

Answer 13

Glucose + NAD + H+ +2ADP +2pi—> 2*Pyruvate + NADH + 2ATP

Question 14

What cells use cellular respiration?

Answer 14

All living organisms respire as it is required for growth, however some organism cannot respire aerobically (mostly bacteria).

Question 15

Alcohol fermentation

• What organisms
• inputs and outputs

Answer 15

plants, fungi, bacteria

2* Pyruvate —–> Ethanol + 2*CO2

Question 16

lactic acid fermentation

• What organisms
• inputs and outputs

Answer 16

Animals

2* Pyruvate —–>Lactic acid

Question 17

Krebs Cycle inputs & Ouputs:

don’t need to know numbers

Answer 17

Inputs: 2 Acetyl CoA, 2 (ADP+Pi), 8 (NAD+ +H+), 2 FAD, 6 O2
Outputs: 2ATP, 6 CO2, 8 NADH, 2 FADH2

Question 18

Electron transport chain Inputs and Ouputs

Answer 18

Inputs; 32 (ADP+pi), 10 NADH, 2 FAD, 6 O2

Outputs: 32 ATP, 10 NAD+, 10 FAD, 6 H20

Question 19

Balanced Photosynthesis equation

Answer 19

6CO2+12H20 ——Energy—–>C6H12O6 + 602 + 6H2O

Question 20

Photosynthesis Light dependant inputs & outputs

Answer 20

Inputs: Light, H2O, NADP+, ADP+Pi
Outputs: 6 O2 + NADPH +ATP

Question 21

Photosynthesis Light independant inputs & outputs

Answer 21

Inputs: 6 CO2 + ATP + NADPH
Outputs: Glucose, H20, ADP+p1, NADP+

Question 22

Hydrogen ion carriers for photosynthesis and respiration

Answer 22

Photosynthesis: NADP+ —>NADPH
Respiration: NAD—NADH
FAD–FADH2

Question 23

Location of light dependant phase of photosynthesis:

Answer 23

Thylakoid membrane.

Question 24

Ganum

Answer 24

Stack of thylakoid disks inside a chloroplast

Question 25

Location of light independant phase of photosynthesis:

Answer 25

stroma (aqueous space)

Question 26

Factors effecting photosynthesis

Answer 26

Co2, O2, H20, chlorophyl levels
Light intensity
temp

Question 27

Why are some plants not green

Answer 27

Plants contain other photopigments which absorb different wavelengths of light.
however all plants contain chlorophyl as it is required for photosynthesis to occur.

Question 28

Key steps light dependant phase of photosynthesis

Answer 28

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

Question 29

Light dependant phase Summary:

Answer 29

• 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.

Question 30

Light independant phase Summary:

Answer 30

• 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.

Question 31

Glycolysis Summary:

Answer 31

6 carbon glucose molecule splits into 2 pyruvate molecules providing the energy for for 2 ATP and NADH to be synthesised.

Question 32

Krebs Cycle Summary:

Answer 32

• 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.

Question 33

Electron transport chain Summary

Answer 33

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.

Question 34

What is rational drug design?

Answer 34

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

Question 35

Compartmentalisation & feedback inhibition in relation to chemical reaction pathways

Answer 35

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