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Notes

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Connor Olsen

on 12 October 2012

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Transcript of Notes

Chapter 1: Pages 1-19 Cell - the lowest structural level in which all of life's properties can occur.
Many molecules of life are arranged into minute structures called organelles (the components of cells).
Population - a localized group of organisms belonging to the same species.
Biosphere - Sum of all Earth's ecosystems.
Reductionism - reducing complex systems to simpler components that are more manageable to study.
Cell Theory - All cells come from other cells.
All cells are enclosed by a membrane that regulates the passage of materials between the cell and its surroundings.
Almost all prokaryotic cells (bacteria) have tough external cell walls.
DNA - substance of genes, the units of inheritance that transmit information from parents to offspring.
Neurons (nerve cells) transmit impulses.
Mitochondria - sites of cell respiration (powers the cell)
First Major Process - Cycling of nutrients
Second Major Process - flow of energy from sunlight to producers to consumers
Platelets cluster to form a clot and seal a wound. Life's Hierarchical Order Biologists have identified and named about 1.5 million species (260,000 plants, 50,000 vertebrates, over 750,000 insects).
Five Kingdoms: Monera (prokaryotic organisms), Protista (unicellular eukaryotes and their relatively similar multicellular relatives), Plantae (plants), Fungi (fungi), Animalia (animals).
Prokaryotes are grouped into Bacteria/Archaea, Eukaryotes are grouped into Eukarya.
Trace Evolution back far enough, and there are only the primeval prokaryotes that inhabited Earth more than three billion years ago.
Evolution - the processes that have transformed life on Earth from its earliest beginning to its vast diversity today.
Darwin Observation #1 - Individuals in a population of any species vary in many heritable traits.
Darwin Observation #2 - Any population of a species has the potential to produce far more offspring than the environment can possibly support with food, space, and other resources.
Descent with modification accounts for both the unity and the diversity we observe in life. Evolution, Unity, and Diversity Hypothesis - an explanation on trial.
Hypotheses are possible explanations.
Hypotheses reflect past experience.
Multiple hypotheses should be proposed whenever possible.
Hypotheses should be testable via the hypothetico-deductive approach.
Hypotheses can be eliminated but not confirmed with absolute certainty.
Technology is like a double-edged sword. It helps us make medicines to make people healthier or to save lives, but it also has increased acid rain, deforestation, global warming, nuclear accidents, ozone holes, toxic wastes, and extinction of species.
"If you are a biology major or a preprofessional student, you have an opportunity to become a versatile scientist. Science is a Process Chapter 2: Pages 22-34 Atom - smallest unit of matter that still retains the properties on an element.
Neutrons have a neutral charge, protons have a positive, and electrons have a negative.
Atomic Nucleus - center of the atom densely packed with neutrons.
We use the measurement "dalton" for things as miniscule as protons and neutrons.
Atomic Number - number of protons in an element.
Mass Number - sum of protons and neutrons in the nucleus of an atom.
Atomic Weight - total mass of an atom.
Isotopes - different atomic forms of an element.
Radioactive Isotope - isotope in which the nucleus decays spontaneously, giving off particles and energy.
Radioactive Isotopes decay to form a different element.
Only electrons are involved in the chemical reactions between atoms.
Energy - the ability to do work.
Potential Energy - the energy that matter stores because of its position or location.
Energy Levels (Electron Shells) - different states of potential energy for electrons in an atom.
Orbital - the 3D space where an electron is found 90% of the time.
Valence Electrons - electrons in the outermost shell.
Valence Shell - the outermost shell.
Atoms with the same number of valence electrons exhibit similar chemical behavior.
Chemical Bonds - attractions (strongest kinds are covalent and ionic).
Covalent Bonds - sharing of a pair of valence electrons by two atoms.
Molecule - two or more atoms held together by covalent bonds.
Structural Formula - notation that represents both atoms and bonding.
Molecular Formula - Symbol to show what element, subscript number to show how many.
Double Covalent Bond - atoms sharing two pairs of valence electrons are joined by these.
Valence - number of unpaired electrons in the atom's outermost shell.
Electronegativity - the attraction of an atom for the electrons of a covalent bond.
Nonpolar Covalent Bond - electrons are shared equally.
Polar Covalent Bond - electrons are not shared equally.
Ion - a charged atom.
Cation - a positively charged ion.
Anion - a negatively charged ion.
Ionic Bond - Bond between two oppositely charged ions.
Ionic Compounds are called salts.
Hydrogen Bond - occurs when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom.
Van Der Waals Interactions - ever-changing "hot spots" of positive and negative charge that enable all atoms and molecules to stick to one another.
Chemical Reactions - the making and breaking of chemical bonds leading to changes in the composition of matter.
Reactants - starting materials in a chemical reaction.
Products - ending materials in a chemical reaction.
Chemical Equilibrium - the point at which the reactions offset one another exactly. Atoms and Molecules Chemical Elements and Compounds Matter - anything that takes up space and has mass.
Element - a substance that cannot be broken down to other substances by chemical reactions.
Compound - a substance consisting of two or more elements combined in a fixed ratio.
About 25 of the 92 natural elements are known to be essential to life.
Carbon (C), Oxygen (O), Hydrogen (H), and Nitrogen (N) make up 96% of living matter.
Trace elements - those required by an organism in only minute quantities. Chapter 3: Pages 37-46 Polar Molecule - opposite ends of the molecule have opposite charges.
Water molecules stick together with hydrogen bonds.
Cohesion - hydrogen bonds hold a substance together.
Adhesion - the clinging of one substance to another.
Surface Tension - a measure of how difficult it is to stretch or break the surface of a liquid.
Kinetic Energy - the energy of motion.
Heat - a measure of the total quantity of kinetic energy due to a molecular motion in a body of matter.
Temperature - measures the intensity of heat due to the average kinetic energy of the molecules.
Celsius Scale - scale used to indicate temperature.
Calorie - the amount of heat energy it takes to raise the temperature of 1g of water by 1 C.
Kilocalorie - the quantity of heat required to raise the temperature of 1 kg of water by 1 C.
Joule - unit of energy.
Specific Heat - the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 C.
Heat must be absorbed in order to break hydrogen bonds.
Heat is released when hydrogen bonds form.
Heat of Vaporization - the quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state.
Evaporative Cooling - As a liquid evaporates, the surface of the liquid that remains behind cools down.
Solution - a liquid that is a completely homogeneous mixture of two or more substances.
Solvent - the dissolving agent of a solution.
Solute - the substance that is dissolved.
Aqueous Solution - one in which water is the solvent.
Hydrophilic - any substance that has an affinity for water.
Hydrophobic - substances that are non-ionic and nonpolar (repel water).
Mole - equal in number to the molecular weight of a substance, but upscaled from daltons to units of grams.
Molecular Weight - the sum of the weights of all the atoms in a molecule.
Molarity - the number of moles of solute per liter of solution. Effects Of Water's Polarity Dissociation of Water Molecules Hydrogen Ion - a single proton with a charge of +1.
Hydroxide Ion - water molecule that lost a proton (has a charge of -1).
Acid - a substance that increases the H+ concentration of a solution.
Base - a substance that reduces the hydrogen ion concentration in a solution.
pH Scale - compresses the range of H+ and OH- concentrations by employing a common mathematical device: logarithms.
Buffers - substances that minimize changes in the concentrations of H+ and OH- in a solution.
Acid Precipitation - refers to rain, snow, or fog more acidic than pH 5.6. Chapter 4: Pages 48-55 Carbon accounts for the endless diversity of biological molecules.
Organic Chemistry - branch of chemistry that specializes in the study of carbon compounds.
Carbon atoms are the most versatile building blocks of molecules.
Electron configuration determines the kinds and number of bonds an atom will form with other atoms.
A carbon atom usually completes its valence shell by sharing electrons with other atoms in four covalent bonds.
Tetravalence - a molecule can branch off in up to four directions.
Co2 is the source of carbon for all the organic molecules found in organisms.
Hydrocarbons - organic molecules consisting only of carbon and hydrogen.
Isomers - compounds that have the same molecular formula but different structures and hence different properties.
Structural Isomers - differ in the covalent arrangements of their atoms.
Geometric Isomers - have all the same covalent partnerships, but they differ in their spatial arrangements.
Enantiomers - molecules that are mirror images of each other. The Importance of Carbon Functional Groups - the components of organic molecules that are most commonly involved in chemical reactions.
The six functional groups most important in the chemistry of life are the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate.
Hydroxyl Group - hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule.
Alcohols - organic compounds containing hydroxyl groups.
Carbonyl Group - consists of a carbon atom joined to an oxygen atom by a double bond.
Aldehyde - if the carbonyl group is on the end of a carbon skeleton.
Ketone - if the carbonyl group is not on the end of a carbon skeleton.
Carboxyl Group - when an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group.
Carboxylic Acids - compounds containing carboxyl groups (organic acids).
Amino Group - consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton.
Amines - organic compounds with this functional group (Amino Group).
Sulfhydryl Group - consists of a sulfur atom bonded to an atom of hydrogen.
Thiols - organic compounds containing sulfhydryls.
Phosphate Groups - have a phosphate ion covalently attached by one of its oxygen atoms to the carbon skeleton. Functional Groups Chapter 5: Pages 58-68 Polymer Principles Macromolecule - covalently connected atoms that form a molecular colossus weighing over 100,000 daltons.
The architecture of a macromolecule helps explain how that molecule works.
Polymer - a long molecule consisting of many identical or similar building blocks linked by covalent bonds.
Monomers - The repeating units that serve as the building blocks of a polymer.
Condensation Reaction - reaction in which two molecules are covalently bonded to each other through loss of a water molecule.
Dehydration Reaction - reaction in which the molecule lost is water.
Enzymes are specialized proteins that speed up chemical reactions in cells.
Hydrolysis - a process that is essentially the reverse of the dehydration reaction.
Each cell has thousands of different kinds of macromolecules; the collection varies from one type of cell to another in the same organism.
Building an enormous variety of polymers from such a limited list of monomers is analogous to constructing hundreds of of thousands of words from only 26 letters of the alphabet. (Arrangement)
Carbohydrates - sugars and their polymers.
Monosaccharides - simplest carbohydrates known as single/simple sugars.
Disaccharides - double sugars, consisting of two monosaccharides.
Polysaccharides - polymers of many sugars.
Glucose is the most common monosaccharide. Carbohydrates - Fuel and Building Material Carbohydrates - sugars and their polymers.
Monosaccharides - simplest carbohydrates known as single/simple sugars.
Disaccharides - double sugars, consisting of two monosaccharides.
Polysaccharides - polymers of many sugars.
Glucose is the most common monosaccharide.
During cell respiration, cells extract the energy stored in glucose molecules.
Glycosidic Linkage - a covalent bond formed between two monosaccharides by a dehydration reaction.
The architecture and function of a polysaccharide are determined by its sugar monomers and by the positions of its glycosidic linkages.
Starch - polymer consisting entirely of glucose monomers (storage polysaccharide of plants).
Plants store starch as granules within cellular structures called plastids, including chloroplasts.
Glycogen - a polymer of glucose that is like amylopectin but more extensively branched.
Cellulose - major component of the tough walls that enclose plant cells.
Cellulose is the most abundant organic compound on Earth.
Few organisms possess enzymes that can digest cellulose.
Chitin - the carbohydrate used by arthropods to build their exoskeletons.
The monomer of chitin is a glucose molecule with a nitrogen-containing appendage. Lipids - grouped together because they have little or no affinity for water.
Fat - constructed from two kinds of smaller molecules: gycerol and fatty acids.
Glycerol is an alcohol with three carbons, each bearing a hydroxyl group.
Fatty Acid - has a long carbon skeleton, usually 16 or 18 carbon atoms in length.
Fats separate from water because the water molecules hydrogen-bond to one another and exclude the fats.
Triacylglycerol - consists of three fatty acids linked to one glycerol molecule.
Saturated Fatty Acid - no double bonds between the carbon atoms composing the tail, then as many hydrogen atoms as possible are bonded to the carbon skeleton.
Unsaturated Fatty Acid - one or more double bonds, formed by the removal of hydrogen atoms from the carbon skeleton.
A diet rich in saturated fats may result in cardiovascular disease.
A gram of fat stores more than twice as much energy as a gram of a polysaccharide, such as starch.
Phospholipids - similar to fats, but they have only two fatty acids rather than three.
Steroids - lipids characterized by a carbon skeleton consisting of four fused rings.
Cholesterol - a common component of animal cell membranes and is also the precursor from which other steroids are synthesized. Lipids - Diverse
Hydrophobic Molecules Gene - unit of inheritance that programs the amino acid sequence of a polypeptide.
DNA - polymer belonging to the class of compounds known as nucleic acids.
Two types of nucleic acids: Deoxyribonucleic acid and Ribonucleic acid.
DNA is the genetic material that organisms inherit from their parents.
RNA controls protein synthesis.
mRNA - interacts with the cell's protein-synthesizing machinery to direct the production of a polypeptide.
DNA -> RNA -> Protein
Ribosomes - the actual sites of protein synthesis.
Nucleotides - monomers that make up the nucleid acid polymers.
Nucleotides are made up of three parts: an organic molecule called a nitrogen base, a pentose (five-carbon sugar), and a phosphate group.
Two families of nitrogenous bases: Pyrimidines and Purines.
Pyrimidine - has a six-membered ring of carbon and nitrogen atoms.
The members of the pyrimidine family are Cytosine (C), Thymine (T), and Uracil (U).
Purines - larger, with the six-membered ring fused to a five-membered ring.
The members of the purine family are Adenine (A) and Guanine (G).
Adenine, Guanine, and Cytosine are found in both types of nucleic acid.
Thymine is found only in DNA and Uracil is found only in RNA.
The pentose connected to the nitrogenous base is Ribose in nucleotides of RNA and Deoxyribose in DNA.
Nucleoside - a nitrogenous base joined to a sugar.
Polynucleotide - a nucleic acid polymer.
In polynucleotides, nucleotides are joined by covalent bonds called phosphodiester linkages between the phosphate of one nucleotide and the sugar of the next.
The linear order of the bases in a gene specifies the amino acid sequence-the primary structure-of a protein, which in turn specifies that protein's three-dimensional conformation and function in the cell.
The DNA molecules of cells actually consist of two polynucleotides that spiral around an imaginary axis to form a Double Helix.
Adenine always pairs with Thymine, and Guanine always pairs with Cytosine.
The two strands of the double helix are complementary, each the predictable counterpart of the other. Nucleic Acids -
Informational Polymers Proteins - account for more than 50% of the dry weight of most cells, and they are instrumental in almost everything organisms do.
Proteins are used for structural support, storage, transport of other substances, signaling from one part of the organism to another, movement, and defense against foreign substances.
Conformation - having a unique three-dimensional shape.
Polypeptides - polymers of amino acids.
A Protein consists of one or more polypeptides folded and coiled into specific conformations.
Amino Acids - organic molecules possessing both carboxyl and amino groups.
When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, an enzyme can join the amino acids by means of a dehydration reaction.
Peptide Bond - Covalent bond resulting from two amino acids forming a polymer.
Polypeptide - a polymer of many amino acids linked by peptide bonds.
Many proteins are globular (roughly spherical), while others are fibrous in shape.
Primary Structure - a proteins unique sequence of amino acids.
Even a slight change in primary structure can affect a protein's conformation and ability to function.
Secondary Structure - coils and folds that are the result of hydrogen bonds at regular intervals along the polypeptide backbone.
Alpha Helix - a delicate coil held together by hydrogen bonding between every fourth amino acid.
Pleated Sheet - two regions of the polypeptide chain lie parallel to each other.
Pleated Sheets make up the core of many globular proteins.
Tertiary Structure - consisting of irregular contortions from bonding between side chains (R groups) of the various amino acids.
Hydrophobic Interaction - as a polypeptide folds into its functional conformation, amino acids with hydrophobic (nonpolar) side chains usually congregate in clusters at the core of the protein, out of contact with water.
Hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains also help stabilize tertiary structure.
Disulfide Bridges - Strong, covalent bonds formed where two cysteine monomers (amino acids with sulfhydryl groups on their side chains) are brought close together by the folding of the protein.
Quaternary Structure - the overall protein structure that results from the aggregation of polypeptide subunits.
A polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a three-dimensional shape maintained by the interactions respondible for secondary and tertiary structure.
Protein conformation also depends on the physical and chemical conditions of the protein's environment.
Denaturation - protein may unravel and lose its native conformation if the pH, salt concentration, temperature, or other aspects of its environment are altered.
Most proteins become denatured if they are transferred from an aqueous environment to an organic solvent.
Chaperone proteins - molecules that function as temporary braces in assisting the folding of other proteins. Proteins - The Molecular
Tools of the Cell Chapter 7: Pages 102-127 Light Microscope - Visible light is passed through the specimen and then through glass lenses. The lenses refract (bend) the light so the image of the specimen is magnified as it's projected into the eye.
Magnification is how much larger the object appears compared to its real size.
Resolving Power - a measure of the clarity of the image; it is the minimum distance two points can be separated and still be distinguished as two separate points.
Organelles - subcellular structures that are too small to be resolved by the light microscope.
Electron Microscope - focuses a beam of electrons throught the specimen.
Electron beams have wavelengths much shorter than the wavelengths of visible light.
Cell ultrastructure is a cell's anatomy as resolved by an electron microscope.
Transmission Electron Microscope - used for detailed study of the internal structure of cells.
Scanning Electron Microscope - used for detailed study of the surface of the specimen.
Microscopes are the most important tools of cytology (the study of cell structure).
Cell Fractionation - to take cells apart, separating the major organelles so that their individual functions can be studied.
The centrifuge is used to fractionate cells.
Ultracentrifuges - spin as fast as 80,000 rpm and apply forces on particles of up to 500,000 times the force of gravity.
Homogenization is the disruption of cells.
Cell Fractionation enables the researcher to prepare specific components of cells in bulk quantity in order to study their composition and functions. How We Study Cells A Panoramic View
Of the Cell Every organism is composed of either prokaryotic or eukaryotic cells.
Prokaryotic Cell - has no nucleus.
Nucleoid - concentration of genetic material in prokaryotic cells.
Eukaryotic Cell - has a true nuclueus enclosed by a membranous nuclear envelope.
Cytoplasm - the entire region between the nucleus and the membrane bounding the cell.
Cytosol - semifluid medium that are located organells of specialized form and function.
Most bacteria are 1 to 10 micrometers in diameter.
Eukaryotic cells are typically 10 to 100 micrometers in diameter.
Plasma Membrane - functions as a selective barrier that allows sufficient passage of oxygen, nutrients, and wastes to service the entire volume of the cell.
Membranes of various kinds are fundamental to the organization of the cell.
Biological membranes consist of a double layer of phospholipids and other lipids. The Nucleus and Ribosomes Nucleus - contains most of the genes that control the eukaryotic cell.
The nuclear envelope is a double membrane.
A pore complex lines each pore and regulates the entry and exit of certain large macromolecules and particles.
Nuclear Lamina - a netlike array of protein filaments that maintains the shape of the nucleus.
The nuclear matrix is a framework of fibers extending throughout the nuclear interior.
Chromatin - Material organized of DNA and proteins.
Chromosomes - Stringy, entangled, coiled up chromatin.
Nucleolus - where components of ribosomes are synthesized and assembled.
Ribosomes - the sites where the cell makes proteins.
Cells that have high rates of protein synthesis have a particularly large number of ribosomes.
Cells that specialize in protein secretion frequently have a high proportion of bound ribosomes.
Endomembrane System - membranes that are related either through direct physical continuity or by the transfer of membrane segments as tiny vesicles.
The endomembrane system includes the nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, various kinds of vacuoles, and the plasma membrane.
Endoplasmic Reticulum - membranous labyrinth so extensive that it accounts for more than half the total membrane in many eukaryotic cells.
Smooth ER - cytoplasmic surface lacks ribosomes. Synthesizes lipids, metabolizes carbohydrates, and detoxifies drugs and poisons.
Rough ER - appears rough because ribosomes stud the cytoplasmic surface of the membrane. Makes secretory proteins, is a membrane factory that grows in place by adding proteins and phospholipids.
Glycoproteins - proteins that are covalently bonded to carbohydrates.
Transport Vesicles - vesicles in transit from one part of the cell to another.
Golgi Apparatus - products of the ER are modified and stored, and then sent to other destinations.
Two poles of a golgi stack are referred to as the cis and trans faces. These act as the receiving (cis) and shipping (trans) departments of the golgi.
Lysosome - a membrane-bounded sac of hydrolytic enzymes that the cell uses to digest macromolecules.
Phagocytosis - eating by engulfing smaller organisms or other food particles.
Lysosomes use autophagy to recycle the cell's organic material.
Food Vacuoles - Sacs that store food.
Contractile Vacuoles - pump excess water out of the cell.
Central Vacuole - large sac enclosed by a membrane called the tonoplast.
Tonoplast - part of the endomembrane system. In eukaryotic cells, mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work.
Mitochondria - the sites of cellular respiration (the catobolic process that generates ATP by extracting energy from sugars, fats, and other fuels with the help of oxygen.
Chloroplasts - the sites of photosynthesis (found only in plants and eukaryotic algae.
They convert solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis or organic compounds from carbon dioxide and water.
Mitochondria are found in nearly all eukaryotic cells.
Cristae - infoldings inside the mitochondria.
Mitochondria are divided into the intermembrane space and the mitochondrial matrix.
Mitochondrial Matrix - enclosed by the inner membrane.
Plastids - closely related plant organelle to chloroplasts.
Thylakoids - flattened sacs inside the chloroplast.
Grana - thylakoids stacked like poker chips.
Stroma - fluid outside the thylakoid.
Peroxisome - specialized metabolic compartment bounded by a single membrane.
Contain enzymes that transfer hydrogen from various substrates to oxygen, producing hydrogen peroxide as a by-product. Other Membranous Organelles Cytoskeleton - a network of fibers extending throughout the cytoplasm.
Gives mechanical support to the cell and helps maintain shape.
There are three main types of fibers that make up the cytoskeleton.
Microtubules - thickest of the three types, found in the cytoplasm of all eukaryotic cells.
Microfilaments - thinnest of the three types (also called actin filaments).
Intermediate filaments - fibers with diameters in a middle range.
Centrosome - a region located near the nucleus.
Centriole - pairs composed of nine sets of triplet microtubules arranged in a ring.
Cilia - locomotive appendages that occur in large numbers on the cell surface.
Flagella - locomotive appendages that are longer and usually are limited to one/two per cell.
Basal Body - structurally identical to a centriole.
Dynein - very large protein that makes up the arms extending from each microtubule doublet to the next.
Actin - a globular protein that makes up microfilaments.
The stuctural role of microfilaments in the cytoskeleton is to bear tension.
They also are known for their roles in cell motility.
Myosin - thicker filaments used in the contraction of muscles.
Pseudopodia - cellular extensions that a cell extends and flows into during movement.
Cytoplasmic Streaming - a circular flow of cytoplasm within cells.
Intermediate filaments are more permanent structures and are also used for bearing tension. The Cytoskeleton Cell Wall - protects the plant cell, maintains its shape, and prevents excessive uptake of water.
Much thicker than the plasma membrane.
Primary Cell Wall - a relatively thing and flexible wall.
Middle Lamena - a thing layer rich in sticky polysaccharides called pectins.
Secondary Cell Wall - Has a strong a durable matrix that affords the cell protection and support.
Extracellular Matrix - made of glycoproteins excreted by the cell.
Collagen - forms strong fibers outside the cells.
Proteoglycans - glycoproteins of another class that collagen fibers are embedded in.
Fibronectins - bind to integrins that are built into the plasma membrane.
Integrins - receptor proteins that span the membrane and bind on their cytoplasmic side to microfilaments of the cytoskeleton.
Plasmodesmata - channels that cytoplasm passes through and connects the living contents of adjacent cells.
Unifies most plants into one living continuum.
Three main types of intercellular junctions: Tight Junctions, Desmosomes, and Gap Junctions. Cell Surfaces and Junctions Chapter 8: Page 130-144 All biological membranes have selective permeability.
Selective Permeability - allows some substances to cross it more easily than others.
Phospholipids are the most abundant lipids in most membranes.
Amphitpathic - has both a hydrophobic and a hydrophilic region.
Cell membranes are made up of phospholipid bilayers.
Fluid Mosaic Model - membrane proteins are dispersed and individually inserted into the phospholipid bilayer, with only their hydrophilic regions protruding far enough from the bilayer to be exposed to water.
Lipids and proteins in the membrane tend to drift slightly.
Because of kinks where double bonds are located, unsaturated hydrocarbons do not pack together as closely as saturated hydrocarbons.
Membranes must be fluid to work properly.
Proteins determine most of the membrane's specific functions.
Integral Proteins - generally transmembrane proteins, with hydrophobic regions that completely span the hydrophobic interior of the membrane
Peripheral Proteins - not embedded in the lipid bilayer at all; they are appendages loosely bound to the surface of the membrane, often to the exposed parts of integral proteins.
Some membrane proteins are held in place by attachment to the cytoskeleton.
Oligosaccharides - short polysaccharides. Membrane Structure Traffic Across
Membranes The hydrophobic core of the membrane impedes the transport of ions and polar molecules, which are hydrophilic.
Hydrophobic molecules, such as hydrocarbons, carbon dioxide, and oxygen, can dissolve in the membrane and cross it with ease.
Transport Proteins - allowing only a certain substance or class of closely related substances to cross the membrane.
Diffusion - the tendency for molecules of any substance to spread out into the available space.
Any substance will diffuse down its concentration gradient.
Concentration Gradient - where it is less concentrated.
Passive Transport - the diffusion of a substance across a biological membrane.
Hypertonic - the solution with a higher concentration of solutes.
Hypotonic - the solution with a lower solute concentration.
Isotonic - solutions of equal solute concentration.
Osmosis - diffusion of water across a selectively permeable membrane.
In an isotonic environment, the volume of an animal cell is stable.
If the cell is in a solution that is hypotonic to the cell, water will enter faster than it leaves and the cell will swell and lyse (burst).
Osmoregulation - the control of water balance.
When cells with walls are in a hypotonic solution, the wall helps maintain the cell's water balance.
Turgid - very firm.
If the cells and their surroundings are isotonic, there is no net tendency for water to enter, and the cells become flaccid.
Flaccid - limp.
Plasmolysis - plasma membrane pulls away from the wall. Usually lethal.
Facilitated Diffusion - diffusion with the help of transport proteins that span the membrane.
Transport proteins have many of the properties of an enzyme and can be saturated.
Gated Channels - stimulus causes them to open or close.
Facilitated diffusion speeds the transport of a solute by providing an efficient passage through the membrane, but it does not alter the direction of transport.
Facilitated diffusion is considered passive transport because the solute is moving down its concentration gradient.
Active Transport - to pump a molecule across a membrane against its gradient, the cell must expend its own metabolic energy.
Sodium-Potassium Pump - exchanges sodium for potassium across the plasma membrane of animal cells.
Voltage is electrical potential energy.
Membrane Potential - the voltage across a membrane.
Electrochemical Gradient - combination of forces acting on an ion.
Electrogenic Pump - a transport protein that generates voltage across a membrane.
Proton Pump - actively transports hydrogen ions (protons) out of the cell.
Contransport - a single ATP-powered pump that transports a specific solute.
Exocytosis - fusion of vesicles with the plasma membrane.
Endocytosis - the cell takes in macromolecules and particulate matter by forming new vesicles from the plasma membrane. (Reverse of Exocytosis)
Three types of endocytosis: phagocytosis, pinocytosis, and receptor-mediated endocytosis.
Phagocytosis - a cell engulfs a particle by wrapping pseudopodia around it and packaging it within a membrane-enclosed sac large enough to be classified as a vacuole.
Pinocytosis - the cell gulps droplets of extracellular fluid in tiny vesicles.
Receptor-Mediated Endocytosis - proteins with specific receptor sites are embedded in the membrane, exposed to extracellular fluid. Extracellular substances are called ligands.
Ligands - general term for any molecule that binds specifically to a receptor site of another molecule. In the lab "Chemistry of Membranes", we tested which concentration of alcohol would cause the most stress on the biological membranes of beets.
These are the same types of membranes that we are reading about and that you can see in this picture. Making Connections Metabolism, Energy, and Life Chapter 6: An Introduction
To Metabolism Metabolism - an emergent property of life that arises from specific interactions between molecules within the orderly environment of the cell.
Mechanisms that regulate enzymes balance metabolic supply and demand, averting deficits and surpluses of chemicals.
Catabolic Pathways - degradative processes that release energy by breaking down complex molecules to simpler compounds.
Anabolic pathways - consume energy to build complicated molecules from simpler ones.
Transfer of energy from catabolism to anabolism is called energy coupling.
Biogenetics - the study of how organisms manage their energy resources.
Energy - the capacity to do work (move against opposing forces, such as gravity and friction).
Kinetic Energy - energy of motion.
Potential Energy - energy that matter possesses because of its location or structure.
Thermodynamics - the study of the energy transformations that occur in a collection of matter.
Organisms are open systems (they can transfer/gain energy from their surroundings).
First Law of Thermodynamics - the energy of the universe is constant.
Second Law of Thermodynamics - every energy transfer of transformation makes the universe more disordered.
Entropy - measure of disorder, or randomness.
The Quantity of energy in the universe is constant, but its quality is not.
Energy flows into an ecosystem in the form of light and leaves in the form of heat.
Free Energy - the portion of a system's energy that can perform work when temperature is uniform throughout the system.
Free Energy = total energy - (Absolute Temperature x Entropy)
Change in Free Energy = Free Energy Final State - Free Energy Starting State
Exergonic Reaction - proceeds with a net release of free energy. (Change in free energy is negative)
Endergonic Reaction - one that absorbs free energy from its surroundings. (Change in free energy is positive)
Energy Coupling - the use of an exergonic process to drive an endergonic one.
ATP (Adenosine Triphosphate) - closely related to one type of nucleotide found in nucleic acids (Energy).
Phosphorylated Intermediate - more reactive (less stable) than the original molecule.
Nearly all cellular work depends on ATP's energizing of other molecules by transferring phosphate groups.
Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the endergonic process of making ATP. Enzymes - catalytic proteins.
Catalyst - a chemical agent that changes the rate of a reaction without being consumed by the reaction.
Every chemical reaction involves both bond breaking and bond forming.
Free Energy of Activation (Activation Energy) - the initial investment of energy for starting a reaction (the energy required to break bonds in the reactant molecules).
Activation energy is usually provided in the form of heat that the reactant molecules absorb from the surroundings.
An enzyme speeds a reaction by lowering the activation energy barrier.
Substrate - the reactant an enzyme acts on.
Enzymes are proteins, and proteins are macromolecules with unique three-dimensional conformations.
Active Site - typically a pocket or groove on the surface of the protein.
Induced Fit - as the substrate enters the active site, it induces the enzyme to change its shape slightly so that the active site fits even more snugly around the substrate.
The active site may provide a microenvironment that is conducive to a particular type of reaction.
Activity of enzymes is affected by temperature, pH, and particular chemicals.
Each enzyme has optimal temperatures and pH at which it is most active.
Cofactors - nonprotein helpers for catalytic activity.
Coenzyme - cofactor is an organic molecule.
Competitive Inhibitors - reduce the productivity of enzymes by blocking the substrate from entering active sites.
Noncompetitive Inhibitors - do not directly compete with the substrate at the active site. Enzymes Allosteric Site - a specific receptor site on some part of the enzyme molecule remote from the active site.
A single activator or inhibitor molecule that binds to one allosteric site will affect the active sites of all subunits.
Feedback Inhibition - switching off of a metabolic pathway by its end-product, which acts as as an inhibitor of an enzyme within the pathway.
Cooperativity - this mechanism amplifies the response of enzymes to substrates: One substrate molecule primes an enzyme to accept additional substrate molecules.
Structures within the cell help bring order to metabolic pathways. The Control of
Metabolism We experience Kinetic and Potential energy every day of our lives:
When we are sitting in a chair in class and the bell rings, we have the potential (energy) to get up and leave, and the energy becomes kinetic when we do.
We have the potential (energy) to take a bite of food at lunch, and that energy becomes kinetic energy when we do. Making Connections Chapter 9: Pages 147-166 Cellular respiration and fermentation are catabolic (energy-yielding) pathways.
Organic Compounds store energy in their arrangements of atoms.
Fermentation - a partial degradation of sugars that occurs without the help of oxygen.
Cellular Respiration - oxygen is consumed as a reactant along with the organic fuel.
In eukaryotic cells, mitochondria house most of the metabolic equipment for cellular respiration.
Organic Compounds + Oxygen > Carbon Dioxide + Water + Energy
The breakdown of Glucose is Exergonic:
C6H12O6 + 6O2 > 6CO2 + 6H20 + Energy (ATP + heat)
ATP loses a phosphate during phosphorylation and becomes ADP.
Redox Reactions - a transfer of one or more electrons from one reactant to another.
Oxidation - Loss of electrons from one substance in a redox reaction.
Reduction - Addition of electrons to another substance in a redox reaction.
Reducing Agent - Reducing/Adding electrons.
Oxidation Agent - Oxidizing/Removing electrons.
Burning is the rapid oxidation of fuel accompanied by an enormous release of energy as heat.
NAD+(Nicotinamide Adenine Dinucleotide) - functions as an oxidizing agent during respiration.
Electron Transport Chain - breaks the fall of electrons into several energy-releasing steps instead of one explosive reaction.
The chain consists of a number of molecules, mostly proteins, built into the inner membrane of a mitochondrion.
Cellular Respiration - Food > NADH > Electron Transport Chain > Oxygen Principles of
Energy Harvest The first two stages of cellular respiration, glycolysis and the Krebs cycle, are the catabolic pathways that decompose glucose and other organic fuels.
Glycolysis - occurs in the cytosol, begins the degradation by breaking glucose into two molecules of a compound called pyruvate.
Krebs cycle - takes place within the mitochondrial matrix, completes the job by decomposing a derivative of pyruvate to carbon dioxide.
NADH is formed in some redox reactions in glycolysis and the Krebs cycle (when dehydrogenase enzymes transfer electrons from substrates to NAD+).
Electrons are then passed to the electron transport chain and passes these electrons from one molecule to another. Electrons are combined with hydrogen ions and molecular oxygen to form water.
Energy released in each step of the chain is stored in a form the mitochondrion can use to make ATP.
Oxidative Phosphorylation - powered by the redox reactions that transfer electrons from food to oxygen.
Substrate-Level Phosphorylation - enzyme transfers a phosphate group from a substrate to ADP.
Glucose (a six-carbon sugar) is split into two three-carbon sugars.
These smaller sugars are then oxidized, and their remaining atoms rearrange to form two molecules of pyruvate.
Glycolysis is a source of ATP and NADH and also prepares organic molecules (2 pyruvate) for further oxidation in the Krebs cycle.
Acetyl CoA - Compound that pyruvate is converted into upon entering the mitochondrion.
This is what links Glycolysis to the Krebs cycle.
Cytochromes - Protein electron carriers.
The 2-Carbon Acetate (Acetyl CoA) joins the 4-Carbon oxaloacetate to form the 6-Carbon citrate.
6-Carbon Citrate is then degraded back to oxaloacetate.
This cycle releases CO2, forms 1 ATP (substrate-level phosphorylation), and passes electrons to 3 NAD+ and 1 FAD.
ATP Synthase - the enzyme that actually makes ATP.
NADH and FADH2 donate electrons to electron carriers in the electron transport chain by oxidative phosphorylation, creating ATP.
Electrons are then passed to O2 which make it into H2O.
Chemiosmosis - term that highlights the relationship between chemical reactions and transport across a membrane.
Electron transfer causes electron-carrying protein complexes to move hydrogen from matrix to intermembrane space (storing energy).
Hydrogen diffuses back into the matrix through ATP synthase.
This exergonic passage drives the endergonic phosphorylation of ADP.
Oxidation of glucose to CO2 in respiration produces a maximum of about 38 ATP. The Process of
Cellular Respiration Fermentation provides a mechanism by which some cells can oxidize organic fuel and generate ATP without the help of oxygen.
Aerobic - oxygen is present.
Anaerobic - oxygen is not present.
The electrons from NADH made in glycolysis are passed to pyruvate, restoring the NAD+ required to stay glycolysis.
Alcohol Fermentation - pyruvate is converted to ethanol.
Lactic Acid Fermentation - pyruvate is reduced directly by NADH to form lactate as a waste product, with no release of CO2.
Facultative Anaerobes - Organisms that can make enough ATP to survive by either fermentation or respiration.
Yeast and certain bacteria are facultative anaerobes, capable of making ATP by either aerobic respiration or fermentation.
Glycolysis and the Krebs cycle connect to many other metabolic pathways.
These catabolic pathways combine to funnel electrons from all kinds of food molecules into cellular respiration.
Feedback mechanisms control cellular respiration. Cellular respiration is controlled by allosteric enzymes at key points in glycolysis and the Krebs cycle.
Beta Oxidation - breaks the fatty acids down to two-carbon fragments, which enter the Krebs cycle as acetyl CoA. Related Metabolic Processes Chapter 10: Pages 168-185 Photosynthesis
in Nature Plants and other autotrophs are the producers of the bioshpere.
Autotrophs - producers
Heterotrophs - consumers
Autotrophs nourish themselves without ingesting organic molecules.
Photoautotrophs use the energy of sunlight to synthesize organic molecules from CO2 and H2O.
Heterotrophs ingest organic molecules from other organisms to get energy and carbon.
Chloroplasts are the sites of photosynthesis in plants.
Chlorophyll - green pigment located within the chloroplasts.
Mesophyll - tissue in the interior of the leaf.
Stomata - microscopic pores on the leaf.
Chlorophyll contain thylakoid membranes that separate the thylakoid space from the chloroplasts stroma.
Stacks of thylakoids form grana. The Pathways of
Photosynthesis Photosynthesis: 6CO2 + 12H20 + Light Energy > C6H12O6 + 6CO2 + 6H2O
Chloroplasts split water into hydrogen and oxygen, incorporating the electrons of hydrogen into the bonds of sugar molecules.
The light reactions and the Calvin cycle cooperate in converting light energy to the chemical energy of food.
Light reactions - steps of photosynthesis that convert solar energy to chemical energy.
NADP+ (Nicotinamide Adenine dinucleotide phosphate) - temporarily stores the energized electrons.
Light reactions in the grana produce ATP and split water, releasing O2 and forming NADPH by transferring electrons from water to NADP+.
Calvin cycle in the stroma forms sugar from CO2, using ATP for energy and NADPH for reducing power.
Light reactions convert solar energy to the chemical energy of ATP and NADPH.
Light is a form of electromagnetic energy; it travels in waves.
Colors we see are part of the electromagnetic spectrum.
Photophosphorylation - powering the addition of a phosphate group to ADP.
Carbon Fixation - initial incorporation of carbon into organic compounds.
Wavelength - distance between crests of electromagnetic waves.
Photons - discrete light particles.
Pigment goes from ground state to excited state when a photon boosts one of its electrons to a higher-energy orbital.
Absorption Spectrum - graph plotting a pigment's light absorption versus wavelength.
Chlorophyll A/B - types of chlorophyll.
Action Spectrum - profiles the relative performance of the different wavelengths more accurately than an absorption spectrum.
Carotenoids - hydrocarbons that are various shades of yellow and orange.
Photosystems - have light-gathering "antennae complex" consisting of a cluster of a few hundred chlorophyll a, chlorophyll b, and carotenoid molecules.
Reaction center - where the first light-driven chemical reaction of photosynthesis occurs.
Noncyclic Electron FLow - predominant route.
Involves both photosystems and produces NADPH, ATP, and oxygen.
Noncyclic photophosphorylation - ATP synthesis during noncyclic electron flow.
Cyclic Electron Flow - uses photosystem I but not photosystem II.
Produces ATP but no NADPH or oxygen.
Calvin cycle uses ATP and NADPH to convert CO2 to sugar.
Calvin cycle is a metabolic pathway in the chloroplast stroma.
The enzyme rubisco combines CO2 with ribulose biphosphate (RuBP).
Rubisco - enzyme that catalyzes Carbon fixation.
RuBP - a five-carbon sugar.
G3P - three-carbon sugar produced from Calvin cycle (glyceraldehyde 3-phosphate).
Cycle synthesizes G3P by using electrons from NADPH and energy from ATP.
Most G3P is reused in the cycle to reconstitute RuBP.
Some G3P exits the cycle and is converted to glucose and other essential organic molecules.
Alternative mechanisms of carbon fixation have evolved in hot, arid climates.
Plants use stomata to conserve/release water, depending on if the weather is dry, moist, hot, or cold.
Oxygen from the light reactions builds up.
Oxygen substitutes CO2 in the active site of rubisco. The product formed leaves the cycle and is oxidized to CO2 and H2O in the peroxisomes and mitochondria.
C3 Plants - initial fixation of carbon occurs via rubisco; the Calvin cycle enzyme that adds CO2 to ribulose biphosphate.
Photorespiration - occurs in the light and consumes O2.
As O2 concentrations overtake CO2 concentrations within the air spaces of the leaf, rubisco adds O2 to the Calvin cycle instead of CO2. The product splits, and one piece, a two-carbon compound, is exported from the chloroplast. Mitochondria and peroxisomes then break the two-carbon molecule down to CO2.
C4 Plants - preface the Calvin cycle with an alternate mode of carbon fixation that forms a four-carbon compound as its first product.
There are two distinct types of photosynthetic cells:
Bundle-sheath Cells - arranged into tightly packed sheaths around the veins of the leaf.
Mesophyll Cells - More loosely arranged cells between the bundle sheath and the leaf surface.
CAM plants open their stomata during the night, incorporating the CO2 that enters into organic acids, which they store in mesophyll cells. During the day the stomata close, and the CO2 is released from the organic acids for use in the Calvin cycle.
PEP carboxylase - enzyme that adds CO2 to PEP.
Crassulacean Acid Metabolism (CAM) - mode of carbon fixation ^.
Photosynthesis is the biosphere's metabolic foundation.
The organic compounds produced by photosynthesis provide the energy and building material for ecosystems.
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