Biology: Metabolism and Enzymes

Metabolism

• Metabolism is all enzyme-controlled chemical reactions within cells.
• Anabolic pathways build large molecules from smaller ones, requiring energy.
• Catabolic pathways break down large molecules into smaller ones, releasing energy.
• Amino acids form proteins; glucose forms carbon dioxide and water (in presence of oxygen).

Metabolic Pathways

• Irreversible steps maintain stable substance concentrations within cells.
• Reversible steps allow pathways to continue or reverse.
• Alternative routes allow reactions to proceed if necessary enzymes or substrates are unavailable.

Membranes

• Membranes are made of phospholipids and proteins.
• Protein roles include pumps, pores, and enzymes.

Genes & Enzymes

• Gene expression controls metabolic pathways by controlling enzyme production (enzymes are proteins).
• Enzymes are biological catalysts speeding up reactions by lowering activation energy.
• Properties of catalysts: speed up reactions, remain unchanged during reactions.
• Properties of enzymes: work with specific substrates, have active sites with complementary shapes for substrates. Active sites work via induced fit model, making them dynamic and flexible.
• Activation energy is the energy needed for a reaction to start.
• Induced fit describes the shape change of the enzyme's active site to fit the substrate.
• Affinity means chemical attraction between molecules (used in substrate/enzyme relationships).
• Enzymes are specific because they only work with substrates that have a high affinity for their active sites, which need to be complementary.

Enzyme Activity Factors

• Factors that affect enzyme activity include: temperature, pH levels, substrate concentration, and inhibitor presence.

Inhibitors

• Inhibitors decrease the rate of enzyme controlled reactions.
• Competitive inhibitors have a similar shape to substrates and bind to the active site.
• Overcoming competitive inhibition is done by increasing substrate concentration.
• Non-competitive inhibitors bind to sites outside the active site, changing the active site's shape.

Enzyme Activation

• Activator binding allows enzymes to have active shapes.
• End-product (feedback) inhibition stops a pathway as the product builds up

Cellular Respiration

 - Cellular respiration is a series of enzyme-controlled reactions to release energy from food and generate ATP.
 - Aerobic respiration occurs when oxygen is present.
 - Fermentation occurs without oxygen.

Aerobic Respiration Summary Equation

• Glucose + oxygen produces carbon dioxide + water + 38 ATP.

Fermentation Summary Equation (Animals)

• Glucose -> Pyruvate -> Lactate

Fermentation Summary Equation (Plants & Yeast)

• Glucose -> Pyruvate -> Carbon dioxide + Ethanol.

ATP & ADP

• ATP is a high energy chemical compound containing three phosphates.
• ADP is a low energy chemical compound with two phosphates.
• ATP is constantly generated from ADP and Pi

Phosphorylation

• Phosphorylation is the addition of a phosphate to a molecule.

Glycolysis

• Glycolysis is the first stage of respiration.
• Glycolysis occurs in the cytoplasm.
• The stages result in Glucose -> 2 Pyruvate; NAD -> NADH; 2 ATP used in energy investment phase (2ATP net gain)

Citric Acid Cycle (Krebs Cycle)

• The citric acid cycle is the second stage of aerobic respiration.
• It occurs in the matrix of mitochondria.
• It includes reactions producing 2 ATP, NADH, and FADH2.
• Pyruvate -> Acetyl Coenzyme A + CO2

Electron Transport Chain (ETC)

• ETC is the final stage of aerobic respiration that occurs in the inner membrane of mitochondria.
• NADH and FADH2 deliver electrons/hydrogen ions.
• Hydrogen ions flow back into mitochondria producing ATP.
• Oxygen is the final electron acceptor creating water.

Metabolic Rate

• Metabolic rate is the amount of energy used per unit time.

Measuring Metabolic Rate

• Oxygen uptake, heat production, or carbon dioxide production can measure metabolic rate.

Circulatory Systems

• Fish have a single circulatory system.
• Amphibians and reptiles have an incomplete double circulatory system.
• Mammals and birds have a complete double circulatory system.
• Incomplete double circulatory can't fully oxygenate blood as oxygenated and deoxygenated blood mix.

Conformers & Regulators

• Conformers have internal environments reliant on external conditions; have a lower metabolic cost.
• Regulators maintain internal environments; have a higher metabolic cost.

Thermoregulation

• The hypothalamus detects changes and sends nerve impulses to effectors.
• Effectors include sweat glands, arterioles, hair erector muscles, and skeletal muscles.
• In high temps sweat glands are activated causing evaporation of water and cooling.

Dormancy, Hibernation, and Aestivation

• Dormancy is a reduced metabolic rate.
• Hibernation is predictive dormancy for cold temperatures.
• Aestivation is consequential dormancy for hot temperatures.
• Daily torpor refers to cyclical reduced metabolic states in animals like small mammals and birds.

Migration

• Migration is the movement by a species from one location to another.
• Reasons include avoiding conditions such as low food supply or severe weather
• Migration strategies are often tracked via ringing/banding, electronic tagging, colour marking, and GPS signals.

Inherited & Learned Behaviour

• Innate behaviour is inherited; inflexible; automatic.
• Learned behaviour is gained through experience; adaptable.

Microorganisms in Industries

• Microorganisms are important in industries due to their rapid growth and reproduction, high productivity of useful products and their highly adaptable metabolism for a variety of substrates.

Growth Medium

• Growth medium is a mix of chemicals for microorganisms.
• Components of growth medium includes energy sources, raw materials for molecule building
• Growth media can be liquid (broth) or solid (agar).
• Maintaining sterility ensures growth is only from the desired organism.

Aseptic Techniques

• Aseptic techniques are sterile procedures that keep cultures from unwanted contamination.
• Important to control environmental variables like temperature, pH, and oxygen concentration.

Microorganism Growth Phases

• Four phases are lag, exponential, stationary, and death.
• During the lag phase there is very little cell growth as cells adapt to new growth mediums.
• The exponential phase has rapid growth due to optimal conditions and sufficient nutrients
• During the stationary phase the birth rate equals the death rate, meaning no net cell gain or loss.
• In the death phase there is a loss of cells due to insufficient nutrients

Cell Counts

• Viable cell count: only counts active/living cells.
• Total cell count: living and dead cells.

Secondary Metabolism

• Secondary metabolism involves producing chemicals not essential for growth, and provides advantage to the organism e.g. antibiotics.
• Most involved during the stationary phase.

Improving Microorganisms

• Approaches include mutagenesis (introducing mutations to improve specific characteristics) and genetic engineering (recombinant DNA) to enhance characteristics like growth rates and production quantities.

Mutagenesis/Recombinant DNA

• Mutagenesis increases mutation rates through a mutagenic agent, used to improve traits of the organism.
• Recombinant DNA transfers genetic materials (e.g. DNA transfer between species).
• Restriction endonucleases cut DNA into fragments at specific sites for insertion into a plasmid (vector) via complementary sticky ends.
• DNA ligase seals fragments back together.  Vectors must have their origin of replication and other features for insertion and growth in a new organism

Vectors

• A vector is a carrier (e.g., plasmid) for transferring DNA.
• Important characteristics include a selectable marker (gene resistance) to identify cells with the new DNA, an origin of replication, restriction sites, and the ability to self-replicate.
• Limitations of using prokaryotes for eukaryotic gene expression is the folding proteins/polypeptides.

Overcoming Prokaryotic Limitations

• Use eukaryotes, such as yeast, who correctly fold proteins/polypeptides .

Test your knowledge on metabolism, metabolic pathways, and the role of enzymes in biological processes. This quiz covers key concepts including anabolic and catabolic pathways, membrane structure, and the influence of genes on enzyme production. Challenge yourself and deepen your understanding of these essential biochemical processes.