Animal Physiology: Conformity, Proteins, and Evolution

• If internal ion levels in an animal are equal to external conditions, it demonstrates conformity.

Cell Junctions

• Tight junctions act as a fence between the apical and basal regions of a cell membrane.

Protein Degradation

• Proteins are tagged for degradation via the ubiquitin pathway.

Phospholipids

• In cold habitats, fish brain synaptic membranes have greater phospholipid unsaturation.

Protein Folding

• Strong covalent bonds do not contribute to the folding (tertiary structure) of proteins.
• Hydrogen bonds stabilize secondary and tertiary structures.
• Ionic bonds (salt bridges) form between charged side chains.
• Hydrophobic interactions drive protein folding by clustering nonpolar residues inside the protein.

Enzymes

• Interspecific enzyme homologs are different molecular forms of an enzyme coded by homologous gene loci in different species.

Evolution

• Evolution is a change in allele frequency over time.

Feedback Loops

• Negative feedback loops return a system to its original state after a change, exemplified by homeostasis.
• Positive feedback loops cause a system to change further in the same direction, such as contractions during birth.

Biological Clocks

• Biological clocks drive cyclical changes that follow daily, seasonal, or other rhythms, occurring in repeating patterns.

Traits

• Nonadaptive traits occur when an allele with a lower probability of survival and reproduction becomes predominant due to chance.

Amplification

• Multiple-enzyme sequences where each enzyme activates multiple others exemplify amplification.

Covalent Modulation

• Covalent modulation involves attaching or removing a chemical group (e.g., phosphate) from a protein, altering its activity.

Enzyme Affinity

• A lower Km value indicates high substrate affinity of an enzyme.

Cell Function Regulation

• Cell function is regulated through metabolic pathways via enzyme synthesis/degradation and changes to catalytic activity.

Receptors

• G protein-linked receptors are membrane proteins that do not allow chemicals to pass through the membrane.
• Enzyme/enzyme-linked receptors are membrane proteins that activate a catalytic site without chemicals passing through the membrane.
• Intracellular receptors have small, membrane-soluble ligands, are not membrane proteins, and often act as transcription factors.

Location

• Intracellular means within the cell.
• Membrane proteins are located within the membrane

Genomics

• The overarching goal of genomics is to elucidate the evolution and current function of genes and genomes.

Metabolomics

• Metabolomics studies organic compounds in cells/tissues, excluding macromolecules coded by the genome, to elucidate metabolic pathways.

Phospholipids

• Phospholipids have a polar head and a non-polar tail.
• Unsaturated phospholipids have double bonds, causing kinks that prevent close packing and maintain fluidity at lower temperatures.
• Saturated phospholipids have single bonds, allowing close packing and remaining solid at higher temperatures.

Enzymes

• Enzymes are protein catalysts that accelerate reactions by lowering activation energy.
• Ca2+ is Calcium.
• Tight junctions act like a fence between the apical and basal regions of the cell membrane.
• cAMP is cyclic adenosine monophosphate, a second messenger.

RNAseq

• RNAseq analyzes the transcriptome by sequencing and quantifying RNA molecules to characterize it.

Ligand-Gated Channels

• Ligand-gated channels are integral membrane proteins that allow chemicals, such as inorganic ions (Na+, K+), to pass through.
• A channel membrane protein is responsible for the passive movement of K+ across the typical animal cell membrane.

Microvilli

• Microvilli increase surface area and are found in cells active in excretion or reabsorption, also called brush border.
• Venomous animals evolved venoms that break down phospholipids because phospholipids are fundamental to cell membranes.

Cholesterol

• Cholesterol, a lipid, is an essential component of animal cell membranes and a precursor for synthesizing steroids.
• Microvilli are not common to all simple epithelia.

Epithelia

• Epithelia, layers of cells covering internal/external surfaces, have an apical surface, nucleus, and basement membrane.
• Simple epithelia can form tubules and follicles.
• The apical surface of an epithelial cell faces away from the basement membrane.

Enzyme Kinetics

• Reaction velocity is the amount of substrate converted to product per unit of time.
• Vmax is the maximum rate of reaction.
• Km is the substrate concentration required to attain 1/2 Vmax.
• kcat, or turnover number, describes catalytic effectiveness as the number of substrates converted to product when saturated.

Enzymes

• Constitutive enzymes are present in high and steady amounts.
• Inducible enzymes are present at low levels or absent unless activated by inducing agents.
• Protein kinases catalyze the covalent attachment of phosphate groups (phosphorylation) to proteins.

Nutrition

• When dietary protein is inadequate, rats grow up with deficiencies in their ability to learn

Phenotypic Plasticity

• Polyphenism is a type of phenotypic plasticity with discrete outputs, resulting in distinct phenotypes from the same genetic background.

Thermoregulation

• Thermoregulation is the maintenance of body temperature within a functional range.

Epigenetics

• Epigenetic modification alters gene expression.
• Epigenetic marking involves DNA methylation and histone modification.
• Epigenetic transgenerational inheritance is the hereditary transmission of epigenetic changes to successive generations.

Genetics

• A genome is all of an organism's genetic material.
• Annotation is adding direct human interpretation to genetic sequencing data.
• The order of investigation in the traditional, top-down approach is: Animal function → tissue function → tissue-specific proteins → genes

Transcriptomics

• Transcriptomics is the study of RNA patterns, showing many genes up and downregulated in response to different stimuli, and daily transcription cycles.

Microarray

• Microarray is a grid of DNA segments used to test and map DNA fragments, antibodies, or proteins.

Adaptation

• Adaptation is a physiological mechanism or trait resulting from evolution that is advantageous.

Integrative Physiology

• Integrative physiology emphasizes synthesis across levels of biological organization.

Physiological Changes

• Evolutionary changes are physiological changes via altered gene frequencies over generations.

Conformity

• The principal advantage of conformity is very little energy usage.

Cell Boundary

• A cell boundary layer is a thin region surrounding a cell that influences environmental interactions.
• In animal cells, combined concentration and electrical effects cause K+ to leak out.
• Developmental changes are permanent physiological changes programmed during growth.
• Chronic changes are long-term adjustments to prolonged exposure, reversible over days to weeks.
• Acute changes are short-term physiological changes soon after environmental changes, and are reversible.

Genetic Drift

• Genetic drift is the change in allele frequency due to chance events, not natural selection.
• Adaptive evolution increases fitness, while nonadaptive evolution changes allele frequencies without regard to fitness, often due to random events.

Genetic Effects

• The bottleneck effect occurs after a dramatic population reduction.
• The founder effect occurs when a few individuals form a new population with a non-reflective gene pool.
• Phenotypic plasticity allows organisms to adjust to varying environmental factors.

Animal Physiology Questions

• Two central questions of animal physiology are: What is the mechanism? and How did that mechanism evolve?
• Genetic constraint are factors that make populations resistant to evolutionary change.
• Pleiotropy is when a single gene has multiple effects on an individual's phenotype.
• Linkage is when alleles close on a chromosome are inherited together.

Membrane Proteins

• Integral membrane proteins are part of the membrane and cannot be removed.
• Peripheral membrane proteins are associated with the membrane but can be removed.
• Channel proteins permit diffusion or osmosis, creating a direct path for water/solutions.
• Transporter (carrier) proteins bind noncovalently and reversibly with molecules or ions to move them across the membrane.
• Receptor proteins bind noncovalently with molecules, initiating changes in membrane permeability or cell metabolism.
• Structural proteins anchor intracellular elements, create junctions, or establish other structural relations.
• The basal surface is the bottom layer of epithelial tissue that attaches to the basement membrane.
• The basement membrane is a thin, permeable, noncellular matrix beneath basal cell surfaces.

Cell Junctions

• Septate junctions are functionally similar to tight junctions but only occur in invertebrates.
• Desmosomes are anchoring junctions that prevent cells from being pulled apart, strengthen connection where cells meet.
• Gap junctions are intercellular junctions where cytoplasms of two cells communicate through tiny pores.

Proteins

• A protein is a three-dimensional polymer of amino acids connected by strong covalent bonds.
• The primary structure of a protein is covalent bonds between amino acids.
• The tertiary structure of a protein is its overall 3D shape due to interactions of R groups, including hydrogen bonds, ionic bonds, and Van der Waals interactions.

Protein Breakdown

• The ubiquitin-proteasome system uses enzyme-catalyzed reactions to target proteins for destruction, breaking them into amino acids while requiring energy.
• Denaturation is the alteration of a protein's tertiary structur due to stress, disrupting function, but it can be repaired.
• Molecular chaperones repair damage, guide protein folding, and prevent unfolded proteins from aggregating, requiring energy.

Metabolism

• Metabolism is the combination of chemical reactions through which an organism builds up or breaks down materials.
• Reaction velocity is the amount of substrate converted to product per unit of time.

Ligands

• Ligands are molecules that bind specifically to a receptor site of another molecule.
• Allosteric modulation is the alteration of an enzyme's catalytic properties through the binding of non-substrate ligands to regulatory sites.
• Isoenzymes are different molecular forms of an enzyme produced by a single species.
• Metabolic pathways are series of chemical reactions in the cell catalyzed by enzymes.

This lesson covers key concepts in animal physiology including conformity in internal ion levels. It also looks at cell junctions, such as tight junctions, and protein mechanisms like degradation via the ubiquitin pathway, the role of phospholipids, and different aspects of protein folding. Finally, it touches upon enzyme homologs and evolution as a change in allele frequency.