Chapter 3 - Biochemical Pathways and Enzymes

Chapter 3 - Biochemical Pathways and Enzymes

• Biochemical pathways consist of a long chain of chemical reactions necessary for the normal functioning of living systems.

• Pathways are interconnected and multi-stepped; controlled by enzymes.

• Two main types of pathways:

Anabolic Pathways:

• Build larger molecules from smaller ones.

• Require energy input.

Catabolic Pathways:

• Break down larger molecules into smaller units.

• Energy is released

Photosynthesis and Cellular Respiration

• Key processes in the production and utilization of energy in organisms.

• Photosynthesis occurs in (chloroplasts); cellular respiration happens in (mitochondria).

• Essential components include:

Light energy  to Chemical energy (NADPH, ATP).

Reactants: CO2, H2O ->  Products: O2, glucose.

• Overview of the processes:

Light Reactions: Convert light energy into chemical energy with oxygen releasedas a byproduct.

Calvin Cycle: ATP and NADPH to fix CO2 into organic molecules.

Enzyme Characteristics

• Enzymes:

Biological catalysts that speed up reactions by lowering the activation energy required.

Primarily proteins made from amino acids.

Specific to substrates and not consumed in the reaction, which means they can be reused.

Most enzymes catalyse one specific reaction (substrate specificity).

Specific Features of Enzymes

• Active Site:

Region where substrate binds

Complementary in shape to the substrate.

• Types of specificity:

Absolute specificity: One specific substrate.

Bond specificity: Specific types of bonds.

Group specificity: Groups of related substrates.

Enzymatic Reactions

• Reactions catalyzed by enzymes can be reversible, participating in both anabolism (building) and catabolism (breaking down).

• Enzymes end with the suffix '-ase' (e.g., lactase, protease).

• Displayed above the reaction arrow in chemical equations.

Cofactors and Coenzymes

• Coenzymes: Organic molecules aiding enzyme function by participating in the reaction.

  • Examples: NAD+, FAD, and coenzymes change structure during catalysis.

• Cofactors: Both organic or inorganic molecules assisting biochemical transformations, such as metal ions.

• Coenzymes exist in two forms:

High energy (loaded) and Low energy (unloaded).

Coenzyme Function

• Coenzymes facilitate:

  • transfer of atoms/groups of atoms (e.g., hydrogens, phosphate).

Energy transfers during enzymatic reactions.

• Recycling of coenzymes is necessary as they cannot be immediately reused.

Summary

• Enzymes lower activation energy, facilitating both photosynthesis and respiration reactions.

• Specific enzymes are essential for specific reactions in metabolic pathways.

• Examples: Rubisco, ATP synthase, involved in photosynthesis.

Glossary Terms

• Activation Energy: Energy required to start a reaction.

• Active Site: The region of the enzyme where substrates bind.

• Anabolic Reaction: A reaction that builds larger molecules.

• Biochemical Pathway: Series of reactions catalyzed by enzymes in living organisms.

• Catabolic Reaction: A reaction that breaks down substances.

• Catalyst: Substance that accelerates a reaction without being consumed.

• Coenzyme: Organic non-protein substances that help enzymes.

• Cofactor: General term for a non-protein that assists enzyme activity.

Key Terms/Concepts

• Enzyme: A biological catalyst that speeds up biochemical reactions by lowering the activation energy required.

• Coenzyme: A non-protein molecule that assists enzymes in catalyzing reactions.

• Denaturation: The process by which an enzyme loses its functional shape due to extreme conditions, rendering it inactive.

• Competitive Inhibition: A type of enzyme inhibition where an inhibitor competes with the substrate for the active site.

• Non-Competitive Inhibition: An inhibitor binds to an allosteric site, changing the enzyme's shape and affecting substrate binding.

Key Processes

• Photosynthesis: The process by which plants convert solar energy into chemical energy, occurring in chloroplasts, involving light-dependent and light-independent reactions.

• Cellular Respiration: The biochemical pathways that release energy from glucose, converting it into ATP for cellular use.

Key Factors Affecting Enzyme Function

Key Concepts in Enzyme Regulation

·       Feedback Inhibition: A regulatory mechanism where the end product of a pathway inhibits an enzyme involved earlier in the pathway.

·       Reversible Inhibition: Inhibitors that bind weakly and temporarily impair enzyme function.

·       Irreversible Inhibition: Inhibitors that bind strongly and permanently impair enzyme function.

Key Terms in Glossary

• Adenosine Triphosphate (ATP): The primary energy carrier in cells.

• Adenosine Diphosphate (ADP): The product formed when ATP loses a phosphate group.

• Chlorophyll: The green pigment in plants that absorbs light energy for photosynthesis.

• Glycolysis: The metabolic pathway that converts glucose into pyruvate, producing ATP.

Facts to Memorize

• Photosynthesis occurs in chloroplasts.

• Aerobic respiration produces 30 or 32 ATP molecules.

• Anaerobic respiration produces 2 ATP molecules.

• Enzymes can be denatured by extreme temperatures and pH levels.

Reference Information

• Light-dependent reactions and light-independent reactions (Calvin cycle) are the two main stages of photosynthesis.

• Competitive inhibitors compete with substrates for the active site, while non-competitive inhibitors bind to an allosteric site.

Nucleic Acids as Information Molecules

What are Nucleic Acids?

• Biomacromolecules that store and pass on genetic material

• Act as a chemical code for making proteins

• Two types:

DNA

RNA

 (Made of monomers called nucleotides

Structure of Nucleic Acids

Each nucleotide has three parts:

1. Phosphate group

2. 5-carbon sugar (deoxyribose in DNA, ribose in RNA)

3. Nitrogenous base

DNA Structure

• Double helix (twisted ladder shape)

• Sugar-phosphate backbone

• Nitrogenous bases make the "rungs"

DNA Nitrogenous Bases

• Adenine (A)

• Thymine (T)

• Cytosine (C)

• Guanine (G)

Base Pairing Rule

• A pairs with T

• C pairs with G

• Purines (A, G) pair with Pyrimidines (C, T)

Antiparallel Nature of DNA

• DNA strands run in opposite directions (5’ → 3’ and 3’ → 5’)

• Strands are held together by hydrogen bonds

1. mRNA (Messenger RNA)  Carries genetic code from DNA to ribosomes

2. tRNA (Transfer RNA)  Brings amino acids for protein synthesis

3. rRNA (Ribosomal RNA) Forms part of ribosomes