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- Study of function - of cells, organs, systems and organisms.
- Antamoy is related because structure determines function
Levels of Organization
- Organ Systems
- The organs of the body are composed of 4 primary tissues:
- Epithelial: transport specialists, cover and line organs, form glands
- Connective: Connect, anchor, support; few cells dispersed in matrix
- Muscle: Specialized for contraction
- Nerve: Specialized for generation and conduction of electrical events (nerve impulses)
- 10 organ systems
- Skeletal and muscle-movement
- Nerve and endocrine-communication and control
- Digestive and respiratory-nutrient intake
- Ciculatory (cardiovascular and lymphatic) nutrient and hormone delivery, waste removal
- Urinary-metabolic waste removal; salt and water balance
- Immune-includes skin and parts of lyphmatic system; preotects body against microbes
- Reproduction-next generation
- Means constancy of the internal environment, results from regulation via negative feedback loops a variety of parameters essential for life are regulated.
- Regulation occurs in the extracellular fluid which = plasma + interstitial fluid
- Any condition that disrupts homeostasis is a stressor
- When a stressor causes change, balance is restored by negative feedback loops
- NFLs do not prevent variation, they maintain homeostasis; NFL failure leads to illness
3 Components to NFLs
- Sensor-Detects stimulus, a change in the level of one of the above parameters
- Itegrator-receives information about parameter, compares to a set-point, effects a response
- Effector-a muscle or gland that effects a change which restores conditions to normal.
Positive Feedback Loops
Amplify processes, bring them to a rapid conclusion (clotting, birth, orgasm)
Parameters (7 sacred)
- Essential factors necessary for life
- Water-solvent, chemical reactant, body temp tegulation
- Oxygen-oxidize food, pick up electrons at end of cell respiration
- Glucose-(+ essential amino and FAs) supply energy and building blocks for synthesis
- Salts- (ions, electrolytes) essential as messenger molecules and for nerve impulses (Na, K, Ca)
- Heat- necessary for chemical reactions (temperature is the measure of amount of heat present)
- pH- extremes of pH and temperature denature proteins
- Blood pressure- maintain delivery of nutrients to all cells.
Cells perform the following jobs
- Synthesis-of macromolecules from monomer subunits to be used for growth, repair, regulation
- Transport-of substances into and out of cells
- Movement-of muscle, cilia, flagella, ameboid cells, organelles
- Communication-with other cells, via chemical messengers which dock with receptors
The key functional and regulatory molecules are proteins
- Enzymes catalyze synthetic reactions
- Transport proteins determine transport capabilities
- Movement is a result of motor protein interactions
- Chemical messengers dock with protein receptorsProtein structure is the basis of how proteins work and is coded for by DNA
Cell physiology includes the study of
- Cell chemistry: elements, compounds, bonds, biochemistry
- Protein binding: how proteins perform physiological functions
- Protein synthesis: DNA transcription and translation
- Cell Structure: organelles, tissues
- Metabolism: enzymes, energy transformations and chemical reactions
- Cell Membranes: transport, communication and potentials
- Cell Replication: mitosis and meiosis
2 or more atoms bonded together
Have different chemical properties than those of the constrituent elements
Formed when atoms share a pair of electrons
- Formed when one atom captures an electron from another
- Anion-gains an electron, becomes a negatively charge ion
- Cation-loses an electron, becomes a positively charged ion
- Ions dissolved in water can conduct electricity are called electrolytes.
Are a weak electrical attraction between the positive part of one polar molecule and the negative part of another. Hydrogen bonds between water molecules account for many of the essential, life supporting properties of water. They also hold together the DNA double helix and secondary protein structure
- Essential for life
- Serves as coolant, lubricant, protective cushion.
- Essential for hydrolysis reactions which break down large molecules into monomer subunits
- Key to biological solvent and molecules can be grouped by their solubility in water
Hydrophillic and Hydrophobic
- Hydrophillic: Polar substances are soluble in water-salts, sugars, proteins
- Hydrophobic: non polar ones are not-lipids
- This division allows for the existence of cells because membranes can form, and it determines the shape of biological molecules.
- Concentration of solutes in solutions is important, kidneys regulate sale/water balance
- Physiologically relevant descriptions of concentration include molarity and osmolarity
- Molarity moles of solute/liter of solvent. (mole=molecular weight in grams) cytosol is usually 0.3M
- Osmolarity refers to total number of dissolved particles relative to normal cell concentrations
Refers to the hydrogen ion concentration of a solution; a hydrogen ion is a proton
molecules that release hydrogen ions into solutions, proton donors, pH less than 7
Molecules that can combine with hydrogen ions; proton acceptors, pH greater than 7
- Molecules that serve to prevent large changes in pH of solutions.
- They can absorb or release hydrogen ions
- The most important physiological buffers are bicarbonate, phosphates, proteins
- The process by which atoms and molecules interact to form new chemical combinations; bonds are formed, broken, reformed.
- Reactants enter the process
- Products are the result
- Exergonic reactions release energy
- Endergonic reactions require an input of energy
- Chemistry includes several types of molecules with ver different chemical structures, may consits of long chains of hydrocarbons; all are soluble in organic solvents; monomers are fatty acids (fats are solid at room temperature, oils are liquid)
- Triglycerides, Phospholipids, Steroids or as Wilson likes to say "Steeroids")
- 3 fatty acid chains linked to glycerol
- Can be saturated or unsaturated
A phosphate group replaces oe fatty acid chain, phosphate is polar, makes molecule amphipathic (has both polar and non polar region-both hydrophobic and hydrophillic)
- All have a skelteon of 4 interconnected carbon rings; cholesterol is parent molecule prostaglandins: a type of fatty acid, act as paracrine regulators in many physiological processes
- Energy source and energy storage molecules, yield more calories/gram than carbohydrates.
- Phospholipids form cell membranes; cholesterol is steroid hormone precurson and forms bile salts.
There are 20. All have amino group + carboxyl group + R Group
- Amino acids linked by peptide bonds; after there are 50 aa, they are called proteins.
- Proteins have 4 levels of structure-the shape or conformation of proteins determines function
Linear amino acid sequence -this is what genes code for
Conformation of portions of polypeptide chain (alpha helix, pleated sheet, random coil)
The overall conformation of the protein molecule; held together by hydrogen and other weak bonds that form between R groups-therefore extremes of heat and pH denature proteins
2 or more polypeptides joined=functional molecule-a protein; hemoglobin antibodies, many channels and enzymes have quaternary structure
Structural and functional roles of proteins
- Enzyme: pepsin
- Hormone: insulin
- O2 transport: hemoglobin
- Regulatory: Calmodulin
- Contractile: Myosin
The ability to bind various molecules and ions to specific sites on the surface of protein molecules forms the basis for the wide variety of functions performed by proteins (Vander)
A molecule/ion that non covalently binds to a protein
The specidic region to which a ligand binds
- Only one kind or type of ligand will bind
- Each enzyme will only catalyze one reaction, break one specific bond
- Strength of ligand-protein binding
- Strength of reaction between substrate and enzyme
Fraction of binding sites occupied at one time
2 or more ligans compete for 1 site
- Binding (non covalent and reversible) of a regulatory molecule to an allosteric or regulatory site, which is different than the functional site and changes the shape and therefore the activity of the functional site (can turn the protein's function on or off)
- A regulatory molecule attaches to allosteric site and activates enzyme. A cofactor such as Ca binds to activate energy. An end product of a biosynthetic pathway "feeds back" can bind to allosteric site and inhibit reaction
- Phosphorylation of a protein by means of ATP. Catalyzed by a special enzyme: protein kinase (Phosphorylation=covalent binding of high energy phosphate group
- Phosphorylation of enzyme is needed for activation
- Make it when you need it. DOn't make it when you don't.
- Control of enzyme synthesis
- Cells make an enzyme not already present, especially important during development
lipid bilayer surrounding cell
Highly organized, membrane bound structures inside cells
- An organelle, contains DNA-chromosomes and chromatin
- Nucleolous-contains rRNA code, site of rRNA assembly
Portion of cell that is not nucleus
Complex, gel like mass in which organelles are dispersed; primarily water with dissolved salts, monomer and polymer molecules
"energy organelle" produces most of cell's ATP
Workbench where protein synthesis takes place
- A system of membranes; two types
- Rough membranes are covered with ribosomes, functions in protein synthesis, site of protein structure modification: clip, fold, add carbohydrate
- Smooth holds enzymes for lipid synthesis, "molecule transformation" in liver
site for sorting/directing proteins to final destinations
Transfer vehicles for proteins that will be secreted
Membrane bound sacs with hydrolytic or digestive enzymes. This organelle serves as the digestive system of cells, they fuse with products of phagocytosis and worn out organelles and remove them from cells.
Permeatin cytosol is complex protein network. Provides scaffolding to support and organize cellular components and control their movements. The protein fibers that form the cytoskeleton are called microtubules and microfilaments. They anchor free ribosomes which are site of synthesis of proteins used in cytosol itself Microfilaments form the central part of cilia and flagella.
- All material and energy transactions of an organism; all chemical reactions in the body
- The principle metabolic reactions in the body are digestion, intermediary or fuel metabolism, catabolism, anabolism, cell respiration
Process of breaking down macromolecules into monomer subunits by enzymes in GI tract
Intermediary or Fuel Metabolism
All reactions involving degradation, synthesis and transformation of fat, carbo, protein molecules in cells
Cellular breakdown of organic molecules
Cellular synthesis of organic molecules
Oxidative breakdown and release of energy from glucose, other monomers, yielfs ATP
When studying metabolism...
- One is concerned with: energy, matter, the chemical reaction, location
- 1. Extraction of energy from food, channeling that energy into a useful form (ATP) to perform cell work
- 2. Rearrangement of monomer subunits into new biological macromolecules
- 3. Role of enzymes in catalyzing biological reactions
- 4. Role of cell membranes in isolating reactions, substrates, and products
- The capacity to do work
- Comes in many forms-heat, chemical, mechanical, light, electrical
- Animals use chemical energy, derived from sun via plants
- Contained in chemical bonds of fuel (food) molecules
- Laws that govern energy transfers
- 1. Energy is neither created nor destroyed, only converted from one form to another
- 2. When energy is converted, entropy increases (one must supply energy to maintain order)
- Energy is required to make reaction go
- The energy released in exergonic reactions drives endergonic reactions; these reactions are coupled redox reactions-oxidative/reduction reactions.
- Energy is given off during reaction
- The energy released in exergonic reactions drives endergonic reactions; these reactions are coupled redox reactions-oxidative/reduction reactions.
- ADP is phosphorylated as a result of cell respiration
- ATP is then used to phosphorylate a variety of molecules in cells.
- Gives a high energy phosphate group to an acceptor molecule. This is phosphorylation.
- The acceptor is then activated and can carry out cell work. ADP is left over and ATP must be regenerated
- ATP is regenerated using food molecule energy in the process in the process of cell respiration
- Goal of cell respiration
- Input is food + oxygen Output is Water + CO2
- ATP is used by cells to perform cell work: transport, synthesis, movement
- The breakdown of glucose to pyruvate, yields 2 ATPs occurs in cytosol
- Canbe aerobic, pyruvate goes to Krebs Cycle or anaerboic-pyruvate goes to lactic acid
- Strips electrons/protons from pyruvate, remainder of molecule is waste CO2
- Occurs in mitochondria, 2 ATPs are produced; electrons are sent to ETC
Electron Transport Train or oxidative Phosphorylation
- Electrons are passed along a series of carriers
- The energy released is used to transport protons (H) across inner mitochondrial membranes
- The final electron acceptor is oxygen, joins with electrons and protons to form water.
- The transported H forms a gradient which powers ADP to ATP reaction-chemiosmosis.
- Can be used for short bursts of intense activity by humans, when oxygen can be supplied fast enough
- Only glycolysis is used to generate ATP ; pyruvate is changed to lactic acid
- After exertion the oxygen debt must be repaid-lactic acid is re-converted to pyruvate-Kreb Cycle
Synthesis of biological macromolecules, use ATP and monomers to make new macromolecules, synthesis is gentically programmed, excess food is stored as glycogen and fat
- Breakdown of complex biochemical molecules in the body
- Feeds intermediary metabolism
- Body can use protein, carbohydrates and fats to feed Kreb's cycle except brain which can only use glucose
- Activation energy can be reduced by the addition of a catalyst.
- A substance that changes the rate of a reaction without itself being chemically altered in the process
- Catalysts do no change the nature of a reaction or its final result or overall energy balance of a reaction
- Ea is essential in cells-it is a barrier to random reactions
- Biological catalysts, made of proteins, pH and temp labile
- Each one has a specific structure, there are thousands per cell
- They are the primary gene products
- They regulate all synthetic and metabolic activity of cells
- They make possible many reactions and therefore can be used to regulate cell activities
Reactants in enzyme mediated reactions
The site that binds the substrate or ligand
- Part of the enzyme, different from the active site, which binds regulatory or modular molecules.
- This binding results in a change in the conformation of the active site. The change can be activating or inhibitory
Reduction or block in enzyme activity: can be irreversible (poisons form covalent bond with the active site) reversible (physiological inhibitors can react with active site or allosteric site.
Cofactors and coenzymes
Many enzymes are inactive as pure isolated proteins, need cofactors to be active. These are ions (Ca, Mg, Zn) or small organic molecules called coenzymes (derived from vitamins)
Cellular Metabolic Reactions
Must be regulated for ordered growth, differentiation, maintenance and response to environment.
- Occur at the surface of all cells and delineate many organelles
- Cells are the units of life, their milieu (wtf!) is interstitial fluid, which is part of extracellular fluid
- Plasma Membranes are the barriers, gates, and sites of regulation between cells and ECF
- Many functional proteins are anchored in membranes.
- Their functions include:
- Transport-transporters including channels, carriers, pumps
- Communication-receptors recognize and bind specific messenger molecules
- Self markers these proteins identify cells as "self" for protection from immune cells
- Metabolism- an array of enzymes for metabolic pathways can be anchored in sequence
- Structure-cytoskeletal elements anchor to cell membranes
Fluid Mosaic Model
- The structure of cell membranes
- Mosaic-a complex of phospholipid and protein and cholesterol
- Fluid-there are no covalent bonds between the molecules forming the bilayer-allows for flexibility-cells can change shape and not lose structural integrity; pieces of membranes can be added and subtracted (secretory vesicles)
- The integral proteins can move freely in the membrane
Membranes can separate cell from ECF-one organelle from another
The separation created by organelle membranes
- Membranes can create different chemical environments by forming semipermeable barriers to free diffusion and/or actively pumping substances from one compartment to the other
- Can also serve as mixing bowl, holding reactants together
- Many important proteins are anchored there
- Ezymes, receptors, transporters, ID markers, contractile elements, cytoskeletal components