Biology questions

• Key characteristics of life include order within cells, sensitivity to stimuli, reproduction, adaptation, growth, homeostasis, and energy processing.

Cell Theory

• All living organisms are composed of one or more cells.
• Cells are the fundamental units of life.
• New cells arise from the division of pre-existing cells.
• Cells are the building blocks of living organisms.

Importance of Cells

• Cells are the smallest units capable of performing all life functions.
• Key cell functions include nutrient intake, energy production, growth, reproduction, and response to stimuli.
• Cells forming structure enables organismal function and behavior.
• Cell biology is the study of cell structure, function, and behavior.

Composition and Energy in Cells

• All organisms consist of cells.
• Cells use energy to build biological molecules like proteins and fats.
• Membranes maintain separation between intra- and extracellular environments.
• Kinetic energy is movement-related, while potential energy is stored energy in chemical bonds.
• Glucose conversion illustrates potential to kinetic energy transformation.

Biological Energy: Metabolism

• Metabolism encompasses all chemical reactions in an organism involving energy.
• Cellular metabolism comprises reactions in living cells, divided into catabolic and anabolic processes.
• Catabolic reactions convert nutrients to energy.
• Anabolic reactions synthesize larger biomolecules.
• Enzymes act as catalysts speeding up reaction rates.

ATP as an Energy Source

• ATP hydrolysis releases -7.3 kcal/mol for cellular processes.
• Phosphorylation involves ATP transferring a phosphate group, powering cell functions and product formation.

Metabolic Diversity

• Organisms obtain energy from various sources.
• Lithotrophs derive energy from inorganic materials.
• Phototrophs use sunlight.
• Organotrophs depend on organic molecules.

Ecosystems Based on Lithotrophs

• Vent fields feature sulfur bugs and methane makers in mid-Atlantic ridge vent systems.
• Acid pools contain iron bugs in copper mines in Chile.
• Rock caverns house sulfur worms and methane makers in deep mines and boreholes.

The Role of mRNA

• Codons are nucleotide triplets in mRNA that encode information to construct proteins.
• The genetic code is universal; it includes 64 different codons.
• Protein structure is determined by the amino acid sequence, which itself is determined by the genetic code.
• Start codon (AUG) initiates protein synthesis.
• Stop codons (UAA, UAG, UGA) terminate protein synthesis.
• Codons ensure correct amino acid sequence for proper protein function

Genes Encoding Proteins

• Genes encode proteins that regulate cell functions.
• The genes expressed in a cell determine its capabilities.
• Prokaryotic operons contain structural genes for enzymes, controlled by promoters, operators, and regulatory genes.
• RNA polymerase and other enzymes regulate the transcription process.

Lac Operon in E. coli

• The lac operon is a bacterial gene control system that turns on to digest lactose when present and off when absent.
• Structural genes, like lacZ, code for β-galactosidase to break down lactose.
• The promoter gene (P) indicates the RNA polymerase binding site.
• The operator gene (O) binds repressor proteins to block transcription when lactose is absent.
• The regulatory gene (lacI) produces the repressor protein that controls the lac operon.

Protein Regulation of Gene Expression

• Transcription factors bind to DNA to regulate genes, an example is P53, which regulates cell repair.
• Cell signaling involves receptors on cell surfaces triggering pathways that activate or repress genes, impacting glucose metabolism with insulin.
• Proteins control genetic information either by binding to DNA or RNA or using signals to trigger pathways.
• Polynucleotides (DNA and RNA) provide instructions for making proteins.

The Role of Mutation in Evolution

• Mutation, a random event in DNA, is the source of differences between beings and causes evolution.
• Traits within a species are hereditary.
• Evolution favors individuals whose traits promote successful reproduction to help survival.

COX2 Gene

• Mitochondrial genes have been lost in eukaryotic cells over time.
• Modern mitochondrial genomes contain different genes in different organisms.
• MT-CO2 variants are linked to mitochondrial complex 4 deficiency, affecting the respiratory chain.
• Leigh's disease is caused by mutated MT-CO2, due to abnormality/ deficiency of cytochrome oxidase
• The COX2 gene is responsible for the previous diseases

Compartmentalization

• Cells are compartmentalized with plasma membranes made of phospholipid bilayers.
• Membrane separation isolates a cell's metabolic processes, allowing conditions inside the cell to vary from the outside.
• The endosymbiosis theory proposes mitochondria originated when an archaeon engulfed a bacteria, which then evolved into an organelle.

Eukaryotic Cells

• Eukaryotic cells compartmentalize specific functions into the nucleus and organelles.
• Compartmentalization helps improve functions and prevents dangerous molecules entering inside.

Scientific Method

• Observe the natural world.
• Develop a hypothesis.
• Make predictions based on your hypothesis.
• Design and perform experiments to test your predictions.
• Collect data and analyze.
• Determine if the data supports your hypothesis.
• A good hypothesis leads to testable predictions.

Model Organisms

• E. Coli: Used for genetic manipulations due to its fast growth and molecular tool availability.
• Yeast: Simple eukaryotic model, it can grow as haploids and diploids and undergo sexual and asexual reproduction.
• Arabidopsis thaliana: The plant is used as a flowing model organism.
• Nematode Caenorhabditis elegans: Used to study genetics, due to hermaphroditic lifestyle, lifespan, and small genome.
• Drosophila melanogaster: Used for quick and efficient research.
• Mus musculus: model mammal.
• Homospaeins and mus musculus: with mutations in the same orthologous gene (hit)

Eyeless Gene

• Homeotic genes, also known as developmental switches, are named for the mutant version.
• Ectopic expression of homeotic gene results in development in unusual places.

Conservation of Developmental Genes

• Pax-6, known as the fly eyeless gene, results in lack of eyes, if defective.
• Pax-6 regulates all that is needed for the development of an eye.
• Pax-6, in the brain, regulates cell processing and controls eye developmemt.

Capsid vs. Capsomere

• Capsids are protein shells enclosing the genetic material of a virus, assembled from multiple capsomeres.
• Capsomeres are protein subunits that self-assemble into capsid shapes, using minimal energy.

Microtubules

• They are components of the cytoskeleton, made of tubulin dimers.
• Microtubules help in cell shape maintanence.
• Polymerization and depolymererization adds/removes tubulin to the ends.
• Microtubules are important for segregation of chromosomes dring cell dividion.

Cellular Energy in Metabolism

• Anabolism consumes energy to convert food, and limited supply leads to cellular dysfunction.
• Catabolism breaks down complex molecules into simpler ones, releasing energy (exergonic).
• Types of catabolic pathways include glycolysis, oxidation, citric cycle.

Importance of Catabolism

• Energy generation from catabolism is the main energy soruce, ensuring survival and function.
• Homeostasis maintains energy balance with ATP production and consumption.
• Adaptations depend on molecule storage to meet energy needs.
• Insulin, glucagon, and epinephrine influence hormonal control.
• High ATP inhibits glycolysis, while low ATP stimulates catabolic enzymes.

Energy for Life is the Sun

• Photosynthesis converts sunlight into biological molecules.
• Cellular respiration occurs in the mitochondria to break down sugars in the presence of oxygen.

Energy and Thermodynamics

• Gibbs free energy is the relationship between the products gives the amount of energy to do work.
• Reactions spontaneously occur when delta G is negative.
• ATP is used to drive reactions with positive delta G by coupling them to exergonic reactions.

Spontaneous Reactions

• Spontaneous reactions occur without external energy input, and they release free energy.
• It depends on enthalpy, entropy, and emperature.

Exergonic Reactions

• Exergonic reactions occur spontaneously.

Endergonic Reactions

• Endergonic reactions will not occur freely

Enzymes and Ribozymes

• Enzymes are protein catalysts.
• Catalysts speed up reactions.
• Ribozymes are RNA.

Activation Energy

• Activation Energy is needed to start a reatcion so that molecules can achive transition state.
• To overcome activation energy, it can be done by increasing the temperature or adding enzymes.

Enzymes Lower Activation Energy

• Enzymes make it easire to achieve transition state by straining bonds and positioning reactants together.

Enzyme Terminology

• The active site is where reactions take place.
• Substrates are the ones that bind to the active site.
• Enzyme-substrate complex: formed when enzyme and substrate bind.
• Coenzymes are organic molecules that participate in reaction but is unchanged afterward.

Inhibition

• Competitive inhibition occurs within the active site.
• Noncompetitive inhibition lowers vmax.

Chemical Energy To Drive Metabolism

• Autotrophs harvest radiant energy.
• Heterotrophs extraxt energy from food.

Cellular Respiration

• Process that converts the chemical energy in food into energy (ATP).
• Most ATP is produced by mitochondria.
• Aerobic depends on oxygen while anaerobic desnt.

ATP

• ATP stores Energy in the cell and is mostly produces by synthase.
• Synthatse is achived by a motar that produces the energy

Glucose Catabolism

• Cells catabolize organic molecules and produce two ways: level phosphorylation and aerobic respiration.

Glycolysis

• Is a metabloic pathway that converts glucose to puruvate.
• Glycolisis uses 2 mjaor phases (investment phase and payoff phase)
• Purpuse traps the glucose cell.

Glycolysis and Respiration

• After Glycolysis, the cell mus tcontinue respiration in either anerobic or areoboic

Krebs Cycle

• It turns glycosis to puruvate
• Oxidizes gylcose
• produces carboxn dioxide
• colllects high energy enectrons
• electrons are trasport to the electron transport chain

Sample questions about cell biology, energy conversion, cellular metabolism, and model organisms. Covers topics like homeostasis, cell theory, ATP, and the use of C. elegans and S. cerevisiae in research.