Transcription, Enzymes, and Limiting Factors

Metabolism

• Metabolism is the totality of chemical reactions within a cell or organism
• Metabolic reactions have two key functions
  • They provide energy for life processes (e.g., movement, reproduction)
  • They enable the synthesis and assimilation of new organic materials
• Nutrients are converted into new materials and energy (waste is excreted)
• Metabolic reactions can be anabolic or catabolic
  • Anabolism: Building complex macromolecules from simpler biomolecules; requires energy
  • Catabolism: Breaking down macromolecules into simpler molecules; releases energy

Enzymes

• Enzymes are globular proteins that act as biological catalysts, increasing reaction rates
• Enzymes are not consumed by the reaction and can be reused
• Enzyme names often end in "-ase" (e.g., lipase)
• Enzymes catalyze the conversion of reactants (substrates) into products
• The active site of an enzyme is a region on its surface that is complementary in shape and charge to the substrate
• The active site is specific to the substrate
• Enzymes catalyze reactions by lowering the activation energy, threshold (EA)
• Activation energy is the energy required to start a reaction

Enzyme Activity

• Enzyme activity can be measured by the consumption of substrates or formation of products
• Methods to measure include:
  • Measuring pressure change (e.g. catalase)
  • Percentage weight loss (e.g. pectinase)
  • Color change (e.g. pepsin)
  • Mass of precipitate formed (e.g., rennin)
• Factors affecting enzyme activity include:
  • Temperature
  • pH
  • Substrate concentration
  • Enzyme concentration

Catalysis

• Enzyme's active site is not rigid and changes shape to fit the substrate (induced fit model)
• This change in structure promotes catalytic activity
• The conformational changes stress bonds in the substrate and increase reactivity (lower activation energy)

Molecular Collisions

• Enzymes and substrates must collide in the correct orientation to interact
• Increasing kinetic energy and particle concentration increases successful collisions
• Enzymes or substrates can be immobilized (e.g., embedded in a membrane)

Denaturation

• Enzyme activity depends on the 3D shape of the protein (tertiary structure)
• Denaturation breaks the bonds involved in protein folding

Temperature

• Low temperatures limit molecular motion and activation energy
• Increasing temperature increases kinetic energy and the frequency of collisions
  • Peak reaction rate at optimal temperature, dependent on the enzyme
• High temperatures decrease activity due to denaturation

pH

• Changing pH alters enzyme charge, affecting both solubility and shape
• Enzymes have an optimal pH at which activity is highest
• Activity decreases outside this optimal range (denaturation)

Substrate Concentration

• Increasing substrate concentration increases enzyme activity, only up to a point
• At high substrate concentrations, the solution becomes saturated, and all active sites are occupied

Photosynthesis

• Photosynthesis is a process where organisms use light energy to synthesize organic compounds
• Photosynthesis equation: CO₂ + H₂O → C₆H₁₂O₆ + O₂

Light Spectrum

• Photosynthesis uses wavelengths (400-700 nm) within the visible spectrum
• Colors: red, orange, yellow, green, blue, indigo, violet (longest to shortest wavelength)

Photosynthetic Pigments

• Chlorophyll is the primary photosynthetic pigment
• Chlorophyll absorbs red and blue light, reflecting green light
• Absorption spectra shows wavelengths absorbed by pigments
• Action spectra shows wavelengths used in photosynthesis
• Chromatography is a technique to separate pigments by size

Photosynthetic Stages

• Light-dependent reactions convert light energy into chemical energy (ATP)
• Light-independent reactions use this energy to synthesize organic compounds (e.g., glucose)

Carbon Dioxide Enrichment

• CO₂ is a substrate in photosynthesis
• Increasing atmospheric CO₂ can affect global temperatures and rates of photosynthesis
• Experiments (e.g., FACE) can predict outcomes of CO₂ level changes

Limiting Factors of Photosynthesis

• Factors that limit rates: light intensity, wavelengths of light, CO₂ levels, temperature, pH
• Rates are limited by the factor nearest its minimum value

Photosynthesis Experiments

• Experiments measure uptake of inputs (e.g., CO₂) or outputs (e.g., O₂)

Cell Respiration

• Cell respiration is the controlled release of energy from organic compounds (e.g., glucose)
  • This process is primarily used to produce ATP
• Respiration can be either anaerobic or aerobic

ATP

• ATP (adenosine triphosphate) is a molecule that stores chemical energy in its covalent bonds
• It is immediately available as an energy source for cells

Types of Respiration

• Anaerobic respiration partially breaks down organic compounds (e.g., glucose) producing small amounts of ATP and lactate in animals
• Aerobic respiration completely breaks down organic compounds in the presence of oxygen into carbon dioxide and water, producing a larger amount of ATP

Respiration Comparison

• Aerobic respiration produces more ATP than anaerobic
• Aerobic respiration requires oxygen and occurs in mitochondria
• Anaerobic respiration occurs in the cytoplasm without oxygen (sometimes in muscles)

Limiting Factors of Cell Respiration

• Cell respiration is dependent on temperature, pH, glucose concentration, oxygen levels
• Factors near their minimum affect its rate

Transcription and Translation

• The fundamental process of converting genetic information into protein
• Transcription produces RNA from a DNA template (gene)
• Translation produces proteins from an RNA template (mRNA)
• RNA polymerase plays a crucial role in transcription

Mutations

• A gene mutation is a change in the nucleotide structure of a gene
  • Substitution: One base is replaced with another
    • Silent: No change in amino acid
    • Missense: Changes one amino acid
    • Nonsense: Creates a stop codon
  • Insertion/Deletion (frameshift): Adding or removing a base(s), altering the reading frame of codons

Causes of Mutations

• Proofreading errors during DNA replication
• Mutagens (physical, chemical, biological agents) increase mutation rates

DNA Replication

• DNA replication is the process of copying DNA during cell reproduction
• The semi-conservative model describes one old strand and one new strand in each resulting DNA molecule

DNA Technologies

• PCR (polymerase chain reaction) is used to amplify DNA
• Gel electrophoresis separates DNA fragments based on size

Gene Cloning

• Gene cloning introduces a gene into a different organism by using a vector(i.e. plasmid)

Sequencing

• Sanger method is used to determine base sequence in DNA
• The modified PCR process is used to produce DNA fragments with specific lengths

Polygenic Inheritance

• Polygenic traits are influenced by multiple genes and exhibit continuous variation
• Examples include skin color, height

Sex Linkage

• Genes located on sex chromosomes often show different inheritance patterns due to sex bias in genotypes and phenotypes

Pedigree Charts

• Pedigree charts illustrate inheritance patterns across generations.

Phenotypic Plasticity/ Genetic Crosses

• Phenotypic plasticity: how physical characteristics can change due to the environment without changing the genotype
• Genetic crosses: Experiments to demonstrate inheritance principles (like Mendel's pea plant crosses)

Punnett Squares

• Graphic method to predict offspring genotypes and phenotypes from parental crosses

Modes of Inheritance

• Different patterns of how alleles interact to determine traits:
  • Complete dominance, incomplete dominance, co-dominance
  • Sex linkage

Genetic Variation

• Mutations are the only source of new alleles in a population
• Sexual reproduction increases genetic variation
• Genetic variation is crucial for species survival and adaptation