Chapter 6-Metabolism: Energy and Enzymes

6.1 Energy

• energy-capacity to do work
• kinetic energy-energy to do motion
• potential energy-stored energy
• chemical energy-interactions of atoms, one to the other, in a molecule
• laws of thermodynamics
• 1st: law of conservation of energy
• energy cannot be created or destroyed but can only be changed from one form to another
• 2nd:
• energy cannot be changed from one form to another without a loss of usable energy
• entropy-measure of randomness or disorder

6.1 Metabolic Reactions and Energy Transformations

• metabolism-sum of all the reactions that occur in a cell
• reactants-substances that participate in a reaction
• products-substances that form as a result of a reaction
• a reaction will occur spontaneously if it increases the entropy of the universe
• free energy-amount of energy available
• exergonic reactions-reactions where ΔG is negative and energy is released
• endergonic reactions-products have more free energy than reactants, can only occur if there is an input of energy
• coupled reactions-energy released by an exergonic reaction is used to drive an endergonic reaction
• ATP to ADP + is exergonic and energy is released
• ATP (adenosine triphosphate)-common energy currency of cells
• ADP (adenosine disphosphate)-ATP +
• use of ATP as carrier of energy
1. provides a common energy currency that can be used in many different types of reactions
2. when ATP becomes ADP + , the amount of energy released is just enough for biological purposes so little energy is wasted
3. ATP breakdown is coupled to endergonic reactions in such a way that it minimizes energy loss
• 3 uses for ATP
• chemical work
• supplies energy needed to synthesize macromolecules that make up the cell
• transport work
• supplies energy needed to pump substances across the plasma membrane
• mechanical work
• supplies energy needed to permit muscles to contract, cilia and flagella to beat, chromosomes to move, etc.
• ATP is a nucleotide composed of adenine and ribose (adenosine) and 3 phosphate groups
• "high energy" because a phosphate group is easily removed, 7.3 kcal per mole

6.3 Metabolic Pathways and Enzymes

• metabolic pathway-a series of linked reactions beginning with a particular reactant and terminate with an end product
• enzyme-protein molecules that functions as an organic catalyst to speed a chemical reaction
• substrates-reactants in an enzymatic reaction
• energy activation-energy must be added to causes molecules to react with one another
• active site-one small part of the enzyme that complexes with the substrate(s)
• enzyme forms complex with the substrate (ES-complex)
• the enzyme and substrate fit together like a key fits a lock
• induced-fit model-the enzyme is induced to undergo a slight alteration to achieve optimum fit
• some enzymes participate in the reaction
• the presence or absence of an enzyme can determine which reaction takes place
• factors affecting enzymatic speed
• substrate concentration
• more collisions between substrate molecules and the enzyme, but when the active sites are filled continuously, the rate of activity can no longer increase. Maximum rate has been reached
  
• temperature and pH
• more collisions, but if temperature is too high activity levels out and then declines because the enzyme is denatured
  
• enzyme concentration
• enzyme inhibition
• when a product is in abundance, it binds competitively with the active site, but when the product is used up, inhibition is reduced and more product can be produced
• cyanide, penicilllin, poisons
  
• enzyme cofactors
• enzymes require an inorganic ion or organic to function properly
  
• denature-enzyme's chape changes during denaturation, and it can no longer bind its substrates efficiently
• feedback inhibition-when concentration of the product is always kept within a certain range
  
• allosteric site-regulatory binding site on an enzyme that controls the activity of that enzyme
  
• cofactors-necessary ions or molecules, suhc as copper, zinc, or iron (inorganic)
• coenzymes-organic, nonprotein molecules
• vitamins-relatively small organic molcules that are required in trace amounts in our diet and in the diet of other animals for synthesis of coenzymes
• a deficiency in vitamins results in a lack of coenzyme and therefore enzymatic actions (niacin - pellagra, riboflavin - cracks at mouth corners)

6.4 Metabolic Pathways and Oxidation-Reduction

• oxidation-loss of electrons
• reduction-gain of electrons
• photosynthesis
• 6 CO₂ + 6 H₂O + Energy → C₆H₁₂O₆ + 6 O₂
• chloroplasts capture solar energy and convert it by way of an electron transport system
• NADP⁺ (nicotinaminde adenine dinucleotide phosphate)-coenzyme of oxidation-reduction active during photosynthesis
• NADP⁺ + 2e^- + H⁺ → NADPH
• cellular respiration
• C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + Energy
• NAD⁺ (nicotinamide adenine dinucleotide)-a coenzyme involved in oxidations suhc as those that occur during cellular respiration, carrying a positive charge
• NAD⁺ + 2e^- + H⁺ → NADH
• electron transport system-a series of membrane-bound carriers that pass electrons from one carrier to another
• in ETS, each carrier is reduced and then oxidized
• ATP synthase complexes-particles spanning the cell membrane containing a channel that allows hydeogen ions to flow down their electrochemical gradient
• chemiosmosis-the production of ATP due to a hydrogen ion gradient across a membrane

Lecture Notes 10/16-11/15

cell structure and function

development of cell theory

• 1665 Robert Hooke-Royal Society of England
• dead cork cells
• "cell" from cellulae (Latin-"small room")
• 1838 Scheiden "Botanist" stated all plants made of cells
• Schwann "Zoologist" all animals made of cells
• derived that
1. all living things are composed of cells
2. cell is the basic unit of structure/function of life
• 1858 Virchow studied cell division
1. cells come only from preexisting cells
2. life comes from lie

methods of studying cells

• microscopes
• high speed centrifuge/differential centrifugation
• cell size (small) most human cells between 5-20 μ
• determined by surface area to volume ratio
• surface increases by the square (area)
• volume increases by the cube (volume)
• small size needed for volume (where life occurs)
• be able to acquire needed materials through its suface area
• size & shape determined by cell function
• strategies to increase surface area
• folding projections long & thin etc.

major cell types

• prokaryotic cells (before nucleus)
• very small (1-10 microns)
• no membrane bounded organelles
• have cytoplasm, cell membrane, nucleoid region, cell wall
• ex: bacteria, blue-green algae (uniform color)
• eukaryotic cells (true nucleus)
• 4 major cell lines (4 kingdoms)
• Plant, Animal, Fungi, Protista
• all have nucleus and membrane bounded organelles

organelle journey

1. nucleus
• nuclear membrane (double) has huge pores but smaller than DNA
• contains chromatin (DNA + protein)
• becomes chromatin at division
• stains easily (iodine, methylene blue)
  
2. nucleolus
• forms ribosomal DNA
• site of activity in nucleus
3. ribosomes
• RNA and protein
• 2 subunits
• cytoplasmic organelles
• endomembrane system
4. endoplasmic reticulum (ER)
• system of channels and saccules continous with outer layer of nuclear membrane
• rough ER-protein/lipid synthesis, products move to Golgi apparatus
• smooth ER-no ribosomes, may produce lipids and steroid hormones, detoxify drugs in liver (alcohol etc.), muscle cells store Ca⁺⁺, forms transport vehicles
5. Golgi apparatus
• stack of apparatus
• inner face towards ER
• outer face towards cell membranes
• protein filled vesicles from ER move to Golgi to be modified (2, 3, 4 levels of structure and/or lipo or glyco proteins formed here)
6. lysosomes (loose body)
• contain hydrolytic enzymes (40+) "suicide bags"
• digest worn out or foreign molecules
• common in white blood cells
7. microbodies
• similar to lysosomes
• contain specific enzymes-catalase
• peroxisomes-hydrogen peroxide H₂O₂ produced and destroyed by catalase
• glyoxysomes-leaves that photosynthesize germinating seeds to convert lipids into sugars for metabolism
8. vacuoles
• large membrane sac
• large in plants (central vacuole)
• reduces volume of living material
• so improves surface area to volume ratio
• filles with water osmosis-turgor pressure (turgid cells)
• smaller in animals
• storage area for cells
• pigments besides chlorophylls (flowers)
• toxic substances (chemical defense)
9. chloroplasts (anabolic rxns)
• contain pigments of photosynthesis
• double membrane contains thylakoid
• have own DNA, reproduce selves by division
• make some of own proteins
• theory-captured bacteria (symbionts)
10. mitochondria (catabolic rxns)
• double membrane system
• internal membrane folded into cristae
• intermembrane space critical to electron transport and ATP production
• has own DNA (eve theory)
• captured bacteria (symbionts)
• reproduce themselves by divison
11. cytoskeleton
• network of interconnected filaments and tubules from nucleus to plasma membrane maintains cell shape and moves organelles appear and disappear during cell cycle made up of monomers of actin, myosin, tubulin
12. actin and myosin (found in muscles as well as cytoskeleton)
• actin moves organelles around and forms pseudopodia in Amoeboid movement
13. intermediate filaments
• between actin filaments and microtubules
• take part in cell to cell junctions in skin protein keratin which is tough
14. microtubules
• tubulin subunits
• small hollow cylinder about 25 nm from 0.2 to 25 microns in length
• two forms (lambda and beta) forms dimer which is a lambda and beta pair
• forms strings of dimers (doublets) that coil to form tube
  
• 13 rows of dimers
15. centrioles
• 9 triplents arranged in circle with no center
• animal cells have two at right cells
• plants have centrosomes but not centrioles
16. cilia and flagella
• differ by length but have a 9 + 2 circular arrangement
• the 2 are in the center of the 9 microtubule doublets
• eukaryotes have membranes surrounding them but prokaryotes don't

cell membrane

• unit membrane is composed of a phospholipid bilayer with proteins
1. by weight the membrane is 50% lipid and 50% protein
2. hydrophobic fatty acid face inwards
3. hydrophilic phosphate with many different groups attached faces outwards
• E for external environment
• C for cytosol or cytoplasm
4. produced by endoplasmic reticulum with inner face of similar or same composition as E face or outer face of membrane
• phospholipids freely rotate on their long axis in the membrane but seldom flip-flop between layers
• takes ATP energy to do this
• results in the membrane being asymmetrical with distinct inner and outer layers of different protein composition and function
• cholesterol molecules fit between the fatty acid tails
1. reduces permeability of membrane
2. increase stiffness of membrane
3. can flip-flop between layers
• two major methods used to study unit membrane
1. freeze fracture
• freeze a solution of cells (red blood) in liquid nitrogen
• take cube of "ice" and split it with a sharp edge
  
• by chance alone some membrane will be separated between the bilayer
• place sample in a leofelizer to "etch" (freeze dry) it to expose the edge of the membrane
• examine with a scanning electron microscope
• can readily see E face and P (or C) face with proteins embdedded within (E face has glycolipids and proteins, P face has cytoskeletal filaments
1. cell fusion with immunoglobins and florescent dyes
• from cell culture use cells from two different but related species (human and mouse)
• membranes fuse and at first proteins remain separate
• after 30-40 min membrane proteins have completely interspersed with each other
• can move at about 2 μm/sec laterally in membrane
  
• asymmetry makes/allows each side of the membrane to be functionally distinct from each other (mitochondria, chloroplasts), enzyme action one side vs. other side
• disulfide bridges, tertiary bonding, vanderwaal's forced, ionic interactions
  
• membrane proteins
• peripheral proteins (on outside and inside of membrane)
  
• integral proteins
• anchored by covalent bonds or molecular interactions
• pH change or shaking can disrupt them
• integral proteins within membrane
  
• hydrophilic on surfaces and hydrophobic within membranes
• channel proteins-form pores
• carrier proteins-phagocytosis or pinocytosis, selective
• receptor proteins-for protein hormones, vitamins, or lipoproteins that may need to gain entry
• enzymatic proteins-for photosynthesis or respiration, especially electron transport
• LAB-differential centrifugation, segregate parts
• reside: starch grains, provides energy for embryo
• digestion = hydrolysis
• H₂O₂ is an oxidizer
• peroxisomes reduce it to water and oxygen
• presence of oxidizing molecules cause aging
• vacuoles hard to see, mostly salt and water
• turgor pressure-tree roots
• chromoplasts-petals, not green/plastids
• large vacuoles broken into smaller
• different ratios of different colored chromoplasts
• insects-largest group of plant consumers
• plants develop defenses, i.e. caffeine
• anabolism-build up
• catabolism-break down
• chloroplast
• 2-outer eukaryotic, inner prokaryotic
• outer membrane-clear, thylakoid green
• endosymbion theory-mitochondria/chloroplasts-bacteria adapted symbiosis
• monochlonoantibodies
• glamuglobulims
• ave theory-chloroplasts and mitochondria have own DNA
• trace ancetry through mutations
• MTAC = microtubule organizing center
• centrioles produce microtubules
• filaments fasten cells together
• SPM = semipermeable osmosis
• Ψ_s = -iCRT
• microtubule-hollow, 9 sets of triplets
• plants lack centrioles
• centrosomes located in MTOC region
• shaft of glagellum-ring of 9 microtubule doulbets anchored to central pair
• ATP changes shape
• membrane is extension of cytoplasm
• basal body at the bottom, then doublets continue
• cytoplasmic streaming
• animal cell
• hypotonic-burst, lysis
• hypertonic-shrivels, crenation
• Singer and Nicolson-fluid-mosaic model, freeze-fracture of membrane
• asymmetrical phospholipid bilayer
• Gibbs' free energy
• endosymbiosis theory-membrane through invagination
• MMC-major histocompatibility complex
• faciliated diffusion-no ATP
• energy causes protein to change shape
• doesn't take very much
• solute is moving through diffusion until even with membrane
• sodium potassium pump-active transport mechanism
• gradient high → low
• diabetes
• type I-juvenile
• type II-obesity
  

Chapter 5-Membrane Structure and Function


5.1 Membrane Models

• lipid-soluble molecules enter cells more rapidly than water-soluble molecules
• sandwich/unit membrane model: the outer dark layer of the membrane contains protein plus the hydrophilic heads of the phospholipids, and the interior is the hydrophobic tails of these molecules
• fluid-mosaic model-introducted in 1972 by S. Singer and G. Nicolson proposing that the membrane is a fluid phospholipid bilayer in which protein molecules are either partially or wholly embedded. The proteins are scattered throughout the membrane in an irregular pattern that can vary from membrane to membrane

5.2 Plasma Membrane Structure and Function

• phosopholipids-molecules that form the bilayer of cell membranes, with polar hydrophilic heads bonded to two nonpolar hydrophobic tails
• the hydrophilic (polar) heads face the intracellular and extracellular fluids
• the hydrophobic (nonpolar) tails face each other
• glycolipids-lipid in plasma membranes that bear carbohydrate chains attached to hydrophobic tails
• cholesterol-lipid found in animal plasma membranes; related steroids are found in plant plasma membranes
• cholesterol reduces permeability of the membrane to most biological molecules
• peripheral proteins occur either on the outside of inside surface of the membrane or the inside surface; some are anchored to the membrane by covalent bonding, others by noncovalent interactions that can be disrupted by shaking or changing pH
• integral proteins are within the membrane; hydrophobic regions are embedded within the membrane and hydrophilic regions project from both surfaces of the bilayer
• many integral proteins are glycoproteins
• glycoproteins-proteins in plasma membranes that bear carbohydrate chains that project externally, "sugar-coated"
• plasma membrane is asymmetrical
• carbohydrate chains occur only on outside surface and cytoskeletal filaments attach to proteins only on inside surface
• at body temperature, phospholipid bilayer of plasma membrane has olive oil consistency
• the greater the concentration of unsaturated fatty acid residues, the more fluid is the bilayer
• in each monolayer, hydrocarbon tails wiggle, and entire phospholipid molecule can move sideways at a rage averaging about 2 m per second
• proteins are generally free to drift laterally in the fluid lipid bilayer
• fluidity of membrane is needed for the functioning of some proteins
• enzymes become inactive when the membrane solidies
• plasma mebranes of various cells and their organelles each have their own unique collections of proteins
• channel proteins-proteins through which a substance can simply move across the membrane
• carrier proteins-proteins that combine with a substance and help it to move across the membrane
• receptor proteins-proteins with shapes that allow specific molecules to bind to them
• binding molecules can cause proteins to change shape and bring about a cellular response
• enzymatic proteins-proteins that carry out metabolic reactions directly
• peripheral proteins stabilize and shape the plasma membrane
• carbohydrate chains of glycolipids and glycoproteins serve as the "fingerprints" of the cell
• cell-cell recognition
  

5.3 Permeability of the Plasma Membrane

• differentially-selectively
• permeable-can move across the membrane
• macromolecules cannot diffuse across the membrane because they are too large
• ions and charged molecules cannot cross the membrane because they are unable to enter the hydrophobic phase of the lipid bilayer
• noncharged, lipid-soluble molecules such as alcohols and oxygen can cross the membrane with ease by slipping between the hydrophilic heads of the phospholipids and pass through the hydrophobic tails of the membrane
• concentration gradient-gradual decrease in concentration over distance
• oxygen is more concentrated outside because a cell uses oxygen during cellular respiration
• carbon dioxide is more concentrated inside because it is produced when a cell carries out cellular respiration
• macromolecules can cross through vesicle formation
• ions and molecules (amino acids and sugars) cross through transport proteins
• carrier proteins combine with an ion/molecule and then transport it
• channel proteins form a channel that allows ions/charged molecules to pass through
• passive transport does not use chemical energy
• diffusion
• facilitated transport
• active transport requires chemical energy
• active transport
• endocytosis
• exocytosis
• diffusion-movement of molecules from a higher to a lower concentration until equilibrium is achieved and they are distributed equally
• diffusion is a physical process that can be observed with any type of molecule
• solution-fluid (solvent) that contains a dissolved solid (solute)
• solvent-liquid portion of a solution that dissolved the solute
• solute-substance dissolved in a solvent, forming a solution
• gases can diffuse through lipid bilayer (oxygen and carbon dioxide)
• after inhaling, the concentration of oxygen in alveoli is higher than that in blood, so the oxygen diffuses into the blood
• osmosis-diffusion of water into and out of cells
• a thistle tube containing a 10% sugar solution is covered at one end by a differentially permeable membrane and placed in a beaker containing a 5% sugar solution
1. a differentially permeable membrane separates 2 solutions, does not permit passage of solute
2. beaker has more water (lower percentage of solute) and thistle tube has less water (higher percentage of solute) per volume
3. membrane permit passage of water, there is net movement of water from the beaker to the inside of thistle tube
4. concentration of solute in thistle tube is less than 10% because there is now less solute per volume and the concentration of solute in the beaker is greater than 5% because there is now more solute per volume
• osmotic pressure-pressure that develops in a system due to osmosis
• the greater the possible osmotic pressure, the more likely water will diffuse in that direction
• due to osmotic pressure, water is absorbed from the human large intestine, retained by the kidneys, and taken up by capillaries from tissue fluid
• tonicity-degree to which a solution's concentration of solute versus water causes water to move into or out of cells
• isotonic solutions-solute concentration is same on both sides of membrane, no net gain or loss of water
• hypotonic solutions-solutions that cuse cells to swell or burst due to an inake of water, lower of percentage of solute
  
• any concentration of a salt solution lower than 0.9% is hypotonic to red blood cells
• lysis refers to disrupted cells
• hemolysis is disrupted red blood cells
• turgor pressure-swelling of a plant cell in a hypotonic solution
• hypertonic solutions-solutions causing cells to shrink or shrivel due to a loss of water, solution with a higher percentage of solute
• crenation-shrunken red blood cells
• plasmolysis-shrinking of cytoplasm due to osmosis
• carrier proteins-protein that combines with and transports a molecule or ion across the plasma membrane, required for faciliated transport and active transport
• facilitated transport-passage of molecules such as glucose and amino acids across plasma membrane even though they are not lipid-soluble
• active transport-use of a plasma membrane carrier protein to move a molecule/ion from a region of lower to higher concentration, opposing equilibrium and requiring energy ; molecules or ions move through the plasma membrane, accumulating on either side
• sodium-potassium pump-carrier protein in the plasma membrane that moves sodium ions iout of and potassium into animal cells, important in nerve and muscle cells
• passage of salt (NaCl) across plasma membrane is important
• Cl^- crosses plasma membrane because it is attracted by Na⁺
• sodium ions are pumped across and chloride follows
• exocytosis-vesicles formed by the Golgi apparatus carrying a specific molecules fuse with the plasma membrane as secretion occurs
• insulin
• during cell growth, exocytosis is used as a means to enlarge the plasma membrane, whether or not secretion is taking place
• endocytosis-cells take in substances by vesicle formation, a portion of the plasma membrane invaginates to envelop the substance and then the membrane pinches off to form an intracellular vesicle
• phagocytosis-when the material taken in by endocytosis is large (e.g. food particle, another cell)
• phagocytosis is common in unicellular organisms like amoebas and in amoeboid cells like macrophages
• pinocytosis-vesicles form around a liquid or very small particles (blood cells, cells lining kidney tubules or intestinal walls, plant root cells)
• receptor-mediated endocytosis-form of pinocytosis that is specific because it involves use of a receptor protein shaped in such a way that a specific substace (ligand) can bind to it (vitamins, peptide hormones, lipoproteins)
• receptors gather at a coated pit (layer of fibrous protein on the cytoplasmic side). Once the vesicle is formed, the fibrous coat is released and the vesicle appears uncoated
• coated pits are also involved in the transfer and exchange of substances between cells
• receptor-mediated endocytosis is important, ex: in familial hypercholesterolemia, cholesterol is transported in blood by a complex of lipids and proteins called low-density lipoprotein (LDL). Individuals with familial hypercholesterolemia inherit a gene causing them to have a reduced number and/or defective receptors for LDL in their plasma membranes. Instead of cholesterol enterng cells, it accumulated in aterial blood vessel walls, leading to high blood pressure, occluded arteries, and heart attacks

5.4 Modification of Cell Surfaces

• cell wall-structure that surrounds a plant, protistan, fungal, or bacterial cell and maintains the cell's shape and rigidity
• primary cell wall contains cellulose fibrils in which microfibrils are held together by noncellulose substances
• pectins allow the wall to stretch when the cell is growing, noncellulose polysaccharides harden the wall when the cell is mature
• pectins are abundant in the middle lamella (layer of adhesive substances that holds cells together)
• some cells in woody plants have secondary walls, which have greater quantities of cellulose fibrils and layers of cellulose fibrils are laid down at right angles to one another
• lignin is a common ingredient in secondary cell walls
• plasmodesmata-numerous narrow membrane-lined channels passing through the cell wall connecting the cytoplasm of neighboring cells
• an extracellular matrix is a meshwork of insoluble proteins with carbohydrate chains (glycoproteins) that are produced and secreted by animal cells, influences development, migration, shape, and function of cells
• collagen (strength) and elastin fibers (resistance)
• fibronects and luminins are two adhesive proteins that play a dynamic role in influencing the behavior of cells, directing cell migration during development, necessary for production of milk by mammary gland cells, bind to receptors in the plasma membrane and permit communication between the extracellular matrix and cytoplasm
• proteoglycans are glycoproteins whose carbohydrate chains contain amino sugars, providing a rigid packing gel that joins various proteins in the matrix, regulating the activity of signaling sequences that bind to receptors in the plasma protein
• adhesion junctions-internal cytoplasmic plaques
• tight junctions-where plasma membrane proteins actually attach to each other, producing a zipperlike fastening
• gap junction-allows cells to communicate

Chapter 4-Cell Structure and Function


4.1 Cellular Level of Organization

• 1830s Mathias Schleiden stated that all plants are composed of cells and Theodor Schwann stated that all animals are composed of cells
• cell-smallest unit of living matter
• a cell is not only the structural unit but also the functional unit of organs, and, therefore, organisms
• once a cell gets to a certain size, it divides (multicellular organisms grow, unicellular organisms reproduce)
• Rudolf Virchow concluded "every cell comes from a preexisting cell"
• cell theory-all living things are composed of cells, and cells come from other cells
• most cells are smaller than one millimeter
• cells need surface areas large enough to allow adequate nutrients to enter and to rid itself of wastes
• small cells have greater surface area per volume than large cells
• cells that specialize in absorption have modifications that greatly increase the surface area per volume of the cell
• columnar cells along the surface of the intestinal wall have surface foldings called microvilli that increase their surface area

4.2 Bacterial Cells

• bacteria-prokaryotic cells in the domain Bacteria
• prokaryotic cells-lacking a membrane bound nucleus and organelles
• main features of bacterial anatomy: cell wall, capsule or slime layer, flagellum, plasma membrane, cytoplasm, cytosol, ribosomes, nucleoid, plasmids, thylakoids
• cell wall-contains peptidoglycan
• capsule-surrounds cell wall
• slime layer-gelatinous sheath in lieu of a capsule
• flagellum-long, very thin appendages possessed by motile bacterium
• some also have fimbriae, short appendages that help attach them to appropriate surfaces
• plasma membrane-membrane that regulates the movement of molecules into and out of the cytoplasm
• cytoplasm-the interior of the cell, consisting of cytosol and ribosomes
• cytosol-semifluid medium
• ribosomes-small bodies that coordinate the synthesis of proteins
• nucleoid-where innumerable enzymes and chromosome (loop of DNA)/genes are located
• plasmids-small accessory rings of DNA
• thylakoids-(cyanobacteria) membranes of flattened discs containing light-sensitive pigments
• cytoplasm is the site of thousands of chemical
• bacteria are adapted to living in almost any kind of environment and are diversified to the extent that almost any type of organic matter can be used as a nutrient for some particular bacterium

4.3 Eukaryotic Cells

• eukaryotic cells-cells that have a true nucleus, a membrane-bounded structure where DNA is housed with threadlike structures called chromatin
• a membrane is a phospholipid bilayer with embedded proteins
• organelles-small bodies each with a specific structure and function, many are membrane-bounded
• the cytosol, which is a semifluid medium outside the nucleus, is divided up and compartmentalized by the organelles
• compartmentalization keeps the cell organized and keeps its various functions separate from one another
• the cytosol has an organized lattice of protein filaments called the cytoskeleton
• some eukaryotic cells, notably plant cells, have cell walls
• cell wall-supports and protects the cell but does not interfere with the movement of molecules across the plasma membrane; plant cell walls contain cellulose fibris and therefore has a different composition than the cell wall of bacteria
• endosymbiotic relationship (suggested by Lynn Margulis and others)
1. mitochondria and chloroplasts are similar to bacteria in size and in structure
2. both organelles are bounded by a double membrane--the outer membrane may be derived from the engulfing vesicle, and the inner one may be derived from the plasma membrane of the original prokaryote.
3. mitochondria and chloroplasts contain a limited amount of genetic material and divide by splitting. Their DNA is a circular loop like that of bacteria
4. although most of the proteins within mitochondria and chloroplasts are now produced by the eukaryotic host, they do have their own ribosomes and they do produce some proteins. Their ribosomes resemble those of bacteria
5. the RNA (ribonucleic acid) composition of their ribosomes suggests a eubacterial origin for chloroplasts and mitochondria
• nucleus-has a diameter of about 5 µm, prominent structure in eukayotic cell, containg chromatin in nucleoplasm
• chromatin-looks grainy, a network of strands that undergoes coiling into rodlike structures
• chromosomes-rodlike structures containing DNA and much protein, and some RNA
• nucleolus-dark regions of chromatin where ribosomal RNA is produced and where rRNA joins with proteins to form the subunits of ribosomes
• nuclear envelope-double membrane with pores separating the nucleus from the cytoplasm
• nuclear pores-100 nm, permits the passage of proteins into the nucleus and ribosomal subunits outside of the nucleus
• ribosomes are found in both prokaryotes and eukaryotes
• ribosomes are 20 by 30 nm in eukaryotes and slightly smaller in prokaryotes
• ribosomes are composed of two subunits, one large and one small, and each has its own mix of proteins and RNA
• polyribosomes-groups of ribosomes
• in eukaryotic cells some occur free within the cytosol either single or in groups, or attached to the endoplasmic reticulum
• ribosomes are sites of protein synthesis; they receive mRNA from the nucleus and synthesize proteins
• vesicle-tiny membranous sacs where ribosomes are secreted out of the cell
• ribosomes bind to endoplasmic reticulum through receptor proteins which act as docking sites for a particular molecule
• the endomembrane system consists of the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, and several vesicles
• this system compartamentalizes the cell so that particular enzymatic reactions are restricted to specific regions
• membranes that make up the endomembrane system are connected by direct physical contact and/or by the transfer of vesicles from one part to the other
• endoplasmic reticulum-system of membranous channels and saccules (flattened vesicles), physically continuous with the outer membrane of the nuclear envelope
• rough ER-studded with ribosomes on the side of the membrane that faces the cytoplasm, synthesizes and moders proteins
• smooth ER-does not have attached ribosomes, continuous with rough ER, synthesizes phospholipids, steroids, fatty acids; in the testes it produces testosterone, in the liver it detoxifies drugs
• Camillo Golgi discovered the Golgi apparatus in 1898
• Golgi apparatus-stack of three to twenty slightly curved saccules whose appearance can be compared to a stack of pancakes
• in animal cells one side of the stack is directed toward the ER and the other toward the plasma membrane
• Golgi apparatus contains enzymes that alter the carbohydrate chains first attached to proteins in the rough ER
• the Golgi apparatus packages its products in vesicles that depart at the outer face
• some of these vesicles are lysosomes
• lysosomes-membrane bounded vesicles produced by the Golgi apparatus that have a very low pH and powerful hydrolytic digestive enzymes
• lysosomes sometimes break down macromolecules, fusing with these vesicles and being engulfed by white blood cells
• autodigestion is when parts of a cell are digested by its own lysosomes
• apoptosis-programmed cell death
• peroxisomes-membrane-bounded desicles that contain specific enzymes imported from the cytosol
• have enzymes for oxiding small organic molecules with the formation of hydrogen peroxide
• RH2 + O2 → R + H2O2
• in plants, peroxisomes oxidize fatty acids into molecules and carry out a reaction in leaves that releases carbon dioxide that can be used for photosynthesis
• vacuole-large membranous sac
• plant cells have a large central vacuole so filled with a watery fluid that it gives added support to the cell
• vacuoles store substances
• plant vacuoles contain water, sugar, salt, pigments, toxic molecules
• chloroplasts and mitochondria are two eukaryotic membranous organelles that specialize in converting energy to a form that can be used by the cell
• chloroplasts-use solar energy to synthesize carbohydrates
• mitochondria-where broken down carbohydrate-derived products to produce ATP molecules
• photosynthesis is the process by which solar energy is converted to chemical energy within carbohydrates
• solar energy + carbon dioxide + water → carbohydrate + oxygen
• carbohydrate + oxygen → carbon dioxide + water + energy
• when a cell needs energy, ATP supplies it
• chloroplasts, which are about 4-6 μm in diameter and 1-5 μm in length, are plastids
• stroma-fluid enclosed by two membranes bounding the chloroplast containing DNA, enzymes, ribosomes
• thylakoids-interconnected flattened sacs in grana
• grana-stacked up structures containing thylakoids
• mitochondria are 0.5-1.0 μm in diameter and 2-5 μm in length
• mitochondria are also bounded by two membranes
• cristae-invagination of inner membrane, providing a greater surface area to accommodate the protein complexes and other participants in cellular respiration
• matrix-where the cristae project, inner space filled with semifluid membrane that contains enzymes that break down carbohydrate products, releasing energy that is used for ATP production on the cristae, also contains DNA and ribosomes
• cytoskeleton-network of interconnected filaments and tubules that extends from the nucleus to the plasma membrane in eukaryotic cells
• cytoskeleton change into spindles, contain three types of elements: actin filaments, intermediate filaments, microtubules
• actin filaments are long, thin fibers (7 nm in diameter) containing two chains of globular actin monomers twisted about one another in a helical manner
• they form a dense complex web just under the plasma membrane to which they are anchored by special proteins, they are seen in microvilli that project from intestinal cells, their presence most likely accounts for the ability of microvilli to alternately shorten and extend into the intestine; in plant cells they form the tracks along which chloroplasts circulate or stream in a particular direction; the presence of a network accounts for the formation of pseudopods, extensions that allow certain cells to move in an amoeboid fashion
• motor molecules-proteins that can attach, detach, reattach along an actin filament
• in the presence of ATP, myosin pulls actin filaments along
• intermediate filaments (8-11 nm in diameter) are a ropelike assembly of fibrous polypeptides, but the specific type varies according to the tissue
• some support the plasma membrane and take part in the formation of cell-to-cell junctions
• in the skin filaments made of keratin give mechnanical strength
• need to have phosphate added by soluble enzymes
• microtubules-small hollow cylinders 25 nm in diameter and 0.2-25 μm in length made of a globular protein called tubulin
• when assembly occurs, and tubulin molecules come together as dimers and arrange themselves in rows
• regulation of microtubule assembly is under control of a microtubule organizing center/MTOC
• centrosome-the main MTOC, near the nucleus, radiates microtubules that help maintain the shape of the cell and act as the track along which organelles can move
• centrioles-short cylinders with a 9 + 0 pattern of microtubule triplets
• in animal cells and most protists, a centrosome contains 2 centrioles lying at right angles to each other
• before an animal cell divides, the centrioles replicate and the members of each pair are at right angles to one another. Then, each pair becomes part of a separate centrosome that moves apart and organizes the mitotic spindle
• plant and fungal cells have centrosome equivalents but no centrioles, which means they may not be necessary to the assembly of cytoplasmic microtubules
• in cells with cilia and flagella, centrioles give rise to basal bodies that direct microtubule organization
• a basal body may function for a cilium/flagellum like a centrosome does for a cell
• cilia/flagella-hairlike projections that can move either in an undulating fashion (whip) or stiffly (oar)
• cellular paramecia move by cilia, sperm cells have flagella, our respiratory tract has cilia
• in eukaryotic cells, cilia and flagella have 9 microtubule doublets arranged in a circle around 2 central microtubules called the 9 + 2 pattern, moving when the microtubules slide past one another
• each cilium and flagellum has a basal body lying in the cytoplasm at its base and have the same arrangement of microtubule triplets
  

Lecture Notes 9/22-10/15

• p.35 hydroxyl/FUNCTIONAL GROUPS
  
• biochem
• carbohydrates: mono, di, polysaccharides
• lipids: mono, di, triglyceride
• proteins: 20 basic amino acids
• nucleic acids: DNA, RNA
• carbohydrate
• (CH₂O)_n; 3-7 units long
• 3 C → D-glycerose
• 4 C → therose
• 5 C → lyxose, D-xylose, D-arabinose, D ribose
• 6 C → galactose, D-mannose, glucose, fructose
• hexose
• pentose
• heptose
• glucose 3D: boat, chair
• fructose (2x sweet glucose)
• amylose: helical coil glucose (only α 1→4)
• amylase cleave @ branch point
• animal starch: glycogen (more branches), most in muscles
• glycogen smaller than starch (plant)
• lipids: oil, fat
• two subunits: glycerol (3 OH), fatty acid
• # fatty acids: mono, di, tri glycerides
• glycerine
• butyric acid
• (hexanoic) caproic acid
• palmitic (16-C)
• stearic (18-C)
• oleic (18-C) isomers
• 3 types of cellular lipid
• structural lipid-cell membrane, etc.
• neutral fat-stored, males: 15%, females: 21%
• brown fat in infants between scapulas, nape of neck, great vessels in thorax/abdomen for heat production
• essential fatty acid (20 C's), polyunsaturated, tested in animals
• linolenic
• linoleic
• arachidonic
• olive oil: mono and diglyceride
• ectotherm: unsaturated
• homotherm: saturated (beef)
• energy content: fat 9 calories/gram, more C-C & C-H; carbs 4.3 calories/gram, more C-OH
• phospholipids: diglyceride, phosphate at 3rd OH
• major membrane part
• PO4 is water soluble
• fatty acids are hydrophobic (bilayer of phospholipid)
• cholesterol mixed in to give strength to cell membrane, membrane protein and carbohydrates
• waxes: cuticles; long chain fatty acids (30-40 C)
• proline: ring so bends polypeptide chain
• proteins
• building materials (hair, connective tissue, globular protein)
• selective corners in cell membranes, usually globular proteins
• cell recognition, globular w/polysaccharide chains attached
• muscle contraction actin & myosin (most abundant)
• catalysts, enzymes major groups
• control of DNA and gene expression/repressor protein control DNA
• proteins differ in
• # amino acids (usually > 100 AA to be a protein)
• sequence of AA's in protein
• 8 essential amino acids in humans (diet), rest made from enzymes we have
• breaking disulfide bonds-irrevocable denaturation
• dehydration synthesis & hydrolysis
• dehydration 3x for triglycerides, once for each OH
• elongation occurs on carboxyl end (COOH on right)
• buffers= weak acid + salt
• Chemicals that maintain pH values within narrow limits by absorbing or releasing hydrogen ions, prevent rapid shifts which would be harmful to protein structure for biological activity
• Proton donor and acceptor systems serve as buffers preventing marked changes in hydrogen ion concentration (pH).
• Brönsted-Løwry, acids are proton-donors
• life depends on buffers to maintain homeostasis
• examples:
• acetic acid & Na acetate
• H₂O₃ & NaHCO₃
• if base (OH) is added, extra H is dissociated
• phosphate buffers pH 5.3 to 8.0 (range used in enzyme lab), used in biochemical research
• → KH₂PO₄ & Na₂HPO₄
• arterial blood: 7.4
• venal blood: 7.3
• tris: 9.3
• electrophoresis
• stable charge to adjust pH (8.6 higher than isoelectric pt, isoelectric pt charge=0 for proteins/amino acids)
• moving boundary (liquid)
• paper-using paper as a medium
• gel-agaros/polyacrylamide
• uses
• protein separated
• DNA/RNA separates different bp length (resolution)
• factors affecting separation
• size-larger for DNA/RNA
• shape
• each kind of protein has the same charge, distribution based on # of nucleotide bases in the fragment, can separate fragments with only 2 base length difference-resolution
• high concentration gives smaller "pores"
• buffers make sure pH of solution stays at 8.6 during electrophoresis
• milk protein: casine
• levels of structure in proteins (4)
• primary: sequence of AA in chain determined by DNA
• secondary: folding of chain into α helical coil, H bonding between C and O atoms (i.e. hair), or β pleated, chain folds back and forth on itself
• tertiary: side chains interacting along same protein
• hydrophobic: turn in (vanderwaals)
• polar: face out, increase solubility
• acid/base: H-bonds, many stop here
• quaternary: different proteins interact (hemoglobin 2α and 2β)
• disulfide bond-cystein
• ionic bond (acid/base)
• shape of protein affected by
• temperature
• pH
• + or - ions in solution
• odd protons: positive
• heavy metals (lead, mercury, cadmium, etc.)
• lead: +2 valence (Ca²⁺ and Mg²⁺), brain and spinal cord affected most
• tetraethyl lead (octane)
• cellulose most common organic molecule on earth, about 1 trillion tons made yearly
  

Chapter 3-The Chemistry of Organic Molecules

3.1 Organic Molecules

• the most common elements in living things are carbon, hydrogen, nitrogen, and oxygen, which constitute about 95% of body weight
• sameness and diversity of life are dependent upon carbon
• organic molecules-molecules created by the bonding of hydrogen, oxygen, nitrogen, and other atoms to carbon
• organic molecules always contain carbon and hydrogen, have covalent bonds, may be quite large with many atoms, and are usually associated with living organisms
  
• organic molecules characterize structure and function of living things
  
• inorganic molecules-nonliving matter
• inorganic molecules usually contain positive and negative ions, have ionic bonding, always contain a small number of atoms, and are often associated with nonliving matter
• living things are highly organized and are all composed of: carbohydrates, proteins, lipids, and nucleic acids
• carbon has 4 electrons in its outer shell, so it can bond with as many as four other atoms; if the bonds are covalent, they are even stronger
• carbon usually bonds with hydrogen, oxygen, nitrogen, or another carbon atom
• as carbon can bond with itself, carbon chains of various lengths and shapes results
• carbon can also share two pairs of electrons with another atom, giving a double covalent bond
• carbon-to-carbon bonds can result in ring compounds of biological significance
  
• functional groups-clusters of certain atoms that always behave in a certain way that can be attached to the carbon chain
• hydroxyl
• carboxyl
• ketone
• aldehyde
• amino
• sulfhydryl
• phosphate
• hydrophobic-not attracted to water
• molecules composed of only carbon and hydrogen are hydrophobic
• hydrophilic-attracted to water
• polar molecules that are able to interact with other polar molecules are hydrophilic
• since cells are 70-90% water, the ability to interact with and be soluble in water profoundly affects the function of organic molecules in cells
• organic molecules containing carboxyl groups (--COOH) are both polar and acidic, the tend to ionize and release hydrogen ions in solution --COOH → --COO^- + H⁺
• functional groups determine the polarity of organic molecules and also the types of reactions it will undergo
• isomers-molecules with identical molecular formulas but are different molecules because the atoms in each are arranged differently
• four classes of organic compounds in living things are lipids, proteins, carbohydrates, and nucleic acids
• polymers-huge chains of unit molecules (polysaccharides, polypeptides, nucleic acids)
• monomers-unit molecules (monosaccharides/single sugars, amino acids, nucleotides)
• polymers can be so large that they are called macromolecules
• monomers bond through condensation synthesis
• condensation synthesis-a hydroxyl (--OH) is moved from one monomer and a hydrogen (--H) is removed from another, water is given off (condensation) and a bond is made (synthesis).
• condensation synthesis cannot take place unless the proper enzyme is present and the monomers are in activated energy rich form
• polymers are broken down by hydrolysis
• hydrolysis-the reverse of condensation synthesis, water is added, an --OH group from water attaches to one monomer and an --H from water attaches to the other monomer, so water is used to break the bond
• hydrocarbon chains are hydrophobic. When it has an attached ionized functional group such as carboxyl (--COOH), then that end of the molecule is hydrophilic.
• polar molecules (with +/- charges) are hydrophilic... that's why they're attracted to water molecules. Nonpolar molecules are hydrophobic... that's why they're repelled by water (incapable of being dissolved in water).
  

3.2 Carbohydrates

• carbohydrates-molecules that bear many hydroxyl groups (CH₂O)
• monosaccharides (one sugar), disaccharides (two sugars bonded together), polysaccharides (starches like cellulose and glycogen)
  
• sugars and some polysaccharides serve as energy storage compounds
• cellulose is the most abundant organic compound on Earth because it supports plant cell walls
• carbohydrates attached to cell wall surfaces are specific to the individual and antigenic to certain other individuals
• monosaccharides-simple sugars with a carbon backbone of three to seven carbon atoms
• hexoses-the best known sugars with 6 carbons
• glucose-6 carbon sugar in the blood of animals
• fructose-6 carbon sugar found in fruits
• these two are isomers of each other: they both have C₆H₁₂O₆, but differ in structure
  
• structural differences cause molecules to vary in shape, which is very important in determining how molecules interact with one another
• pentoses-5 carbon sugars
• ribose-found in RNA
  
• deoxyribose-found in DNA
• disaccharide-containts two monosaccharides joined by condensation
• lactose-disaccharide that contains galactose and glucose and is found in milk
• maltose-disaccharide composed of two glucose molecules found in the digestive tract as a result of starch digestion
  
• sucrose-disaccharide that contains glucose and fructose; sugar is transported within the body of a plant in the form of sucrose, table sugar
• disaccharides dissolve in water
• polysaccharides-long polymers of monosaccharides formed by condensation synthesis
• the most common polysaccharides in living things are starch, glycogen, and cellulose, which are chains of glucose molecules.. also chitin (modified glucose molecule)
• glycogen-characterized by many branches/side chains of glucose
• starch-fewer branches than glycogen
• branching allows the breakdown of starch and glycogen to proceed at several points simultaneously; once glucose is released, it is used directly as an energy source
• the orientation of the bond in starch and glycogen allows these polymers to form compact spirals, making polymers suitable as storage compounds
• plants stoor sugar as starch within the cell, as roots, and as seeds
• during seed germination, starch is brokwn down into maltose and then glucose which provides energy for growth
• animal cells store extra carbohydrates as glycogen (muscles and liver join glucose molecules), between meals the liver releases glucose to keep the blood concentration of glucose near the normal 0.1% which moves from the blood into cells to participate in cellular metabolism
  
• cellulose-glucose molecules that are joined together differently than in starch and glycogen, the polymers are straight and fibrous, long and unbranched, held together by hydrogen bonding within microfibrils which in turn make up a cellulose fibril
• cellulose fibrils lie parallel in layers, which lie in angles, making plant cell walls stronger
• cotton fibers are almost pure cellulose
• wood contains a high percentage of cellulose
  
• most animals digest little cellulose because digestive enzymes are unable to break the linkage, but it helps the body maintain regularity of elimination
• cattle and sheep have a special stomach chamber, the rumen, where bacteria live that can digest cellulose
• chitin-a polymer of glucose found in the exoskeletons of crabs and related animals like lobsters and insects
• each glucose unit has an amino group attached to it
• suture thread
  

3.3 Lipids

• lipids-fats, insoluble in water because they lack polar groups, most familiar are found in fats and oils
• fats are utilized for insulation and energy reserves
• phospholipids and steroids (can serve as hormones) are components of the plasma membrane
• fats and oils contain fatty acids and glycerol
• fatty acid-a long hydrocarbon chain with a carboxyl acid group at one end
• most contain 16-18 carbon atoms per molecule
  
• because the carboxyl group is polar, fatty acids are soluble in water
• saturated fatty acids-no double bonds between carbon atoms
• unsaturated fatty acids-double bonds in the carbon chain wherever the number of hydrogens is less than two per carbon atom
• glycerol-compound with three hydroxyl (--OH) groups, soluble in water
  
• when a fat is formed, the acid portions of fatty acids react with these hydroxyl groups, resulting in water molecules
• condensation synthesis reaction, fat can be hydrolyzed to its components
• triglycerides-some fats and oils; there are three fatty acids per glycerol molecule, they lack polar groups and do not mix with water
• triglycerides containing fatty acids with unsaturated bonds melt at an even lower temperature than those containing faty acids with saturated bonds
• double bonds makes a kink that prevents close packingin general, fats are solid at room temperature and of animal origin and oils are liquid at room temperature and of plant origin
• nearly all animals use fat in preference to glycogen for long-term energy storage
• waxes-long chain fatty acids bonded with long-chain alcohol
• waxes are solid at normal temperatures because they have a high melting point, hydrophobic, waterproof, resistant to degradation
• cuticle
• skin, fur maintenance, ear wax
• honey comb
  
• phospholipids-constructed like neutral fats except with a phosphate group or a grouping containing phosphate and nitrogen in place of a third fatty acid
• the phosphate group becomes the polar head, while the hydrocarbon chains become the nonpolar tails
• the plasma membrane which surrounds cells is a phospholipid bilayer in which the polar heads face outward into a watery mdeium and the tails face each other because they are water repelling
• steroids-lipids that have an entirely different structure than that of fats, as they have a backbone of four fused carbon rings, each differing primarily by the types of functional groups attached to the rings
• cholesterol is a component of animal cells plasma membranes and the precursor of several other steroids, such as estrogen and testosterone

3.4 Proteins

• protein-composed of one or more polypeptides (polymers of amino acids)
• proteins perform many functions
• support: keratin, which makes up hair and nails; collagen, lends support to ligaments and tendons; skin
• enzymes: bring reactants together and speed chemical reactions in cells, specific for one particular type of reaction and can function at body temperature
• transport: channel proteins in the plasma membrane allow substances to enter and exit cells, carrier proteins transport molecules into and out of the cell or in the blood of animals (e.g. hemoglobin, which transports oxygen)
• defense: antibodies are proteins that combine with antigens/foreign substances to prevent antigens from destroying cells and upsetiting homeostasis
• hormones: regulatory proteins that serve as intercellular messengers that influence the metabolism of cells, insulin regulates the content of glucose in blood and in cells (e.g. the presence of growth hormone determines the height of an individual)
• motion: contractile proteins actin and myosin allow parts of cells to move and cause muscles to contract, which accounts for the movement of animals from place to place
• vertebrate cells function differently according to the type of protein they contain
• muscle cells contain actin and myosin
• red blood cells contain hemoglobin
• support cells contain collagen, etc.
  
• amino acid-a carbon atom bonded to one hydrogen atom and in addition three groups of atoms (amino group --NH2, acidic group --COOH, and R remainder of the molecule)
  
• amino acids differ according to their R group
• there are 20 different amino acids commonly found in cells because there are 20 different R groups
  
• peptide bond-the resulting covalent bond between two amino acids joined by a condensation reaction between the carboxyl group of one and the amino group of another
• the atoms associated with the peptide bond share the electrons unevenly because oxygen is more electronegative than nitrogen, so the hydrogen attached has a slightly positive charge while the oxygen has a slightly negative charge; this polarity means that hydrogen bonding is possible between the --CO of one amino acid and the --NH of another amino acid in a polypeptide
• peptide-two ore more amino acids bonded together
• polypeptide-chain of many amino acids joined by peptide bonds
• a protein can have up to four levels of structure
• fibrous proteins have to specific tertiary structure and many proteins have no quaternary sutrcture
• the primary structure of a protein is the sequence of the amino acids joined by peptide bonds
• when amino acids join together a polypeptide results, the primary structure is a polypeptide with its own particular sequence of amino acids
• 1953, Frederick Sanger determined the amino acid sequence of the hormone insulin by first breaking insulin into fragments and then determining the amino acid sequence of the fragments before determining the sequences of the fragments themselves
• the secondary structure of a protein occurs when segments of a polypeptide coil or fold in a particular way
• Linus Pauling and Robert Corey concluded that the coiling was an α helix and the pleated sheet was called a β sheet in the late 1930s
  
• hydrogen bonding holds the secondary structure in place
• for the α helix, hydrogen bonding between every fourth amino acid accounts for the spiral shape of the helix
• for the β sheet, the polypeptide turns back upon itself and hydrogen bonding occurs between extended lengths of the polypeptide
  
• in keratin, α helices are covalently bonded to one another by disulfide linkages (--S--S--) between two cysteine amino acids. When you get a perm, the hair is rolled and a reducing agent is used to break the present disulfide bonds, which become two --SH groups instead. When the agent is removed, newly formed disulfide bonds make the hair curly
• tertiary structure is a folding and twisting that results in the final 3-D shape of a polypeptide
• hydrogen bonds, ionic bonds, and covalent bonds all contribute to the tertiary structure of a polypeptide
• strong disulfide linkages help maintain the tertiary shape
• hydrophobic reactions are when hydrophobic R groups don't bond with other R groups and instead collect in a common region where they are not exposed to water, and though they aren't bonds they are very important in creating and stabilizing the tertiary structure
• some proteins have a quaternary structure because they consist of more than one polypeptide, such as hemoglobin
• temperature and pH can bring about a change in polypeptide shape
• the addition of acid to milk causes curdling
• heating causes egg white, which consists mainly of a protein called albumin, to congeal/coagulate
• denatured-a protein that has lost its normal configuration
• denaturation occurs because the normal bonding patterns between parts of a molecule have been disturbed
• each type of enzyme is specific to the reaction it speeds
• when an enzyme is denatured it can no longer bring the substrates, which are the reactants, together for the reaction to occur
• enzymes work best at body temperature and each one also has an optimal pH at which the rate of the reaction is highest, at which it has its normal shape
• a change in pH can change the polarity of R groups and disrupt the normal interactions that maintain the normal shape of the enzyme
• if the conditions which caused denaturation were not too severe, and these are removed, some proteins regain the normal shape and biological activity

3.5 Nucleic Acids

• nucleic acids-polymers of nucleotides with very specific functions in cells
• DNA (deoxyribonucleic acid)-genetic material that stores information regarding its own replication and the order in which amino acids are to be joined to make a protein
• RNA (ribonucleic acid)-another type of nucleic acid, important in the process of protein synthesis
• mRNA is an intermediary
• ATP (adenosine triphosphate)-a nucleotide that supplies energy for synthetic reactions and for various other energy-requiring processes in cells
• nucleotide-complex of three types of molecules: phosphate (phosphoric acid), a pentose sugar, and a nitrogen-containing base
• in DNA the pentose sugar is deoxyribose
• in RNA the pentose sugar is ribose
  
• the base of a nucleotide can be a pyrimidine with a single ring or a purine with a double ring
• in DNA the bases are cytosine and thymine
• in RNA the bases are uracil and cytosine
• in both DNA and RNA the purine bases are adenosine or guanine, they are called bases because their presence raises pH
• nucleotides join in a definite sequence when DNA and RNA form by condensation synthesis
• polynucleotide-a linear molecule called a strand in which the backbone is made up of a series of sugar-phosphate-sugar-phosphate olecules
• since the nucleotides occur in a definite order, so do the bases, which project to one side of the backbone
• RNA is single stranded
• DNA is double stranded in the shape of a double helix
• the two strands are held together by hydrogen bonds between pryimidine and pruine bases
• complementary base pairing
  
• thymine is always paired with adenine
• guanine is always paired with cytosine
• ATP-a nucleotide in which adenosine is composed of adenine and ribose
• ATP is a high-energy molecule because the last phosphate bonds are unstable and easily broken
• in cells the terminal phosphate bond is hydrolyzed to give the molecule ADP (adenosine diphosphate) and a molecule of inorganic phosphate
• the energy released by ATP breakdown is coupeld to energy requiring processes in the cell
• synthesis of macromolecules (carbohydrates and proteins)
• muscle contraction
• conduction of nerve impulses
  
• ATP is sometimes called the energy bond, symbolized by a wavy line, ebcause it releases energy when the last phosphate bonds are hydrolyzed, but the products of hydrolysis are more stable than ATP (ADP and inorganic phosphate)
• the entire molecule releases energy, not just the bond
  

Chapter 2-Basic Chemistry

2.1 Chemical Elements

• matter-anything that takes up space and has mass
• matter can exist as a solid, liquid, or gas
• elements-basic substances that cannot be broken down to substances with different properties (a property is a physical or chemical characteristic, such as density, solubility, melting point, and reactivity)
• only 92 naturally occurring elements
• 6 elements: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur make up the body weight of most organisms (CHNOPS)
• atoms-tiny particles
• early 1800s, John Dalton proposed elements contain one type of atom individually
• atomic symbol-one or two letters that stand for the element's name (H for hydrogen, Na for natrium/sodium in Latin)
• most stable subatomic particles: proton, neutron, electron
  
• proton-positive subatomic particle, located in the nucleus and having a weight of approximately one atomic mass unit
• neutron-neutral subatomic particle, located in the nucleus and having a weight of approximately one atomic mass unit
• electron-negative subatomic particle, moving about in an energy level around the atom
• most of an atom is empty space
• atomic mass-sum of protons and neutrons
• mass is constant while weight changes according to gravitational force
• atomic number-number of protons
• the atomic number is written as a subscript while the atomic mass is written as a superscript
• isotopes-atoms of the same element that have the same number of protons and differ only in the number of neutrons
• radioactive isotopes-an isotope that emits radiation in the form of radioactive particles or radiant energy when decaying
• radioactive isotopes are used in medicine since they are absorbed by metabolically active tissues and can be tracked (PET, positron emission tomography)
• 1913, Niels Bohr proposed that electrons orbit in concentric energy levels about the nucleus; although electrons have the same mass and charge, they vary in energy content
• electron shells-energy levels
• electrons differ in amount of potential energy, and the shells indicate the relative amounts of stored energy electrons have: electrons with the least amount of potential energy are located in the K shell, closest to the nucleus, then L and M
• it takes energy to keep an electron farther away from the nucleus as opposed to closer to the nucleus
• octet rule-outer shell is most stable when it has eight electrons
• atoms with eight electrons normally do not react and are inert
• orbital-volume of space where a rapidly moving electron is statistically predicted to be found
• electrons occupy an orbital rather than orbit
• an orbital has a characteristic energy state and a characteristic shape
• at the first energy level, at most two electrons are found about the nucleus in a single spherical orbital because the most likely location for each electron is a fixed distance in all directions from the nucleus
• at the second energy level, there are four orbitals and a maximum of eight electrons; one is spherical but the other three are dumbbell shaped, which allows electrons to be the most distant from one another
  
• when bonding occurs, the orbitals of the L shell sometimes hybridize, forming teardrop-shaped orbitals that point to the corners of a triangular pyramid called a tetrahedron
• photosynthesis: 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂
• equation is balanced

2.2 Compounds and Molecules

• molecules can form when two or more atoms of the same element react with one another
• compound-when two or more different elements react or bond together (O₂, H₂O is a compound that contains the elements hydrogen and oxygen)
• molecule-the smallest part of a compound that still has the properties of that compound
• ionic bonds form when electrons are transferred from one atom to another
• electron transfers may cause a charge imbalance in each atom
• ions-charged particles
• ionic bond-attraction between charged ions
• covalent bond-when two atoms share electrons in such a way that each atom has an octet of electrons in the outer shell
• molecules have a three-dimensional shape that determines their biological function
• hormones have shapes that allow them to be recognized by the cells in the body
• one form of diabetes occurs when the receptors of cells fail to recognize the hormone insulin
• AIDs occurs when blood cells have receptors that bind to the HIV virus, allowing it to enter, multiple, and destroy the cell
• nonpolar covalent bond-when the sharing of electrons between two atoms is fairly equal
• polar covalent bond-the unequal sharing of electrons in a covalent bond
• in the case of water, the sharing of electrons between oxygen and each hydrogen is not completely equal; the larger O atom has a greater number of protons and thus dominates the association, as it is more electronegative than the hydrogen atom and can attract the electron pair to a greater extent, assuming a negative charge (δ^-) and caushing the hydrogen atoms to assume a slightly positive charge (δ⁺)
  
• electronegativity-the attraction of an atom for the electrons of a covalent bond
• hydrogen bond-an attractive force creating a weak bond
• in water
• a hydrogen bond is more easily broken than a covalent bond, but many hydrogen bonds together are quite strong and help maintain proper sutrcture and function of cellular molecules

2.3 Chemistry of Water

• the first cells evolved in water, and all living things are 70-90% water
• water is a polar molecule and water molecules are hydrogen bonded together
• taken together, hydrogen molecules cause water molecules to cling together
• because of hydrogen bonding, water boils at 100°C and freezes at 0°C
• the temperature of water rises and falls more slowly than other liquids under the same conditions
• a calorie is the amount of heat energy needed to raise the temperature of one gram of water 1C
• the many hydrogen bonds that link water molecules help water absorb heat without a great change in temperature
• water has a high heat of vaporization and thus a high boiling point
• hydrogen bonds must be broken to change water to steam
• water facilitates chemical reactions bother outside of and within living systems
• water dissolves a lot of things because it is polar
• when a salt, such as NaCl, is put into water the negative ends of the water molecules are attracted to the sodium ions and the positive ends of the water are attracted to the sodium ions, and the positive ends of the water molecules are attracted to the chloride ions, causing the sodium ions and the chloride ions to separate and to dissociate in water
• water is also a solvent for larger molecules that contain ionized atoms or are polar molecules
• when ions and molecules disperse in water, they move about and collide, allowing reactions to occur
• hydrophilic-(molecules) attracting water
• hydrophobic-(nonionized and nonpolar molecules that) cannot attract water
• water molecules are cohesive and adhesive
• water molecules flow freely, but do not separate from each other; they cling to each other because of hydrogen bonding, and because they have poles, they adhere to surfaces and particularly polar surfaces
• water can fill a tubular vessel and still flow, dissolved and suspended molecules are evenly distributed throughout a system
• water is an excellent transport system both outside of and within living organisms
• one-celled organisms rely on external water to transport nutrient and waste molecules
• multicellular organisms often contain internal vessels in which water serves to transport nutrients and wastes
• the liquid portion of our blood is 90% water that contains dissolved and suspended substances
• contributes to the transport of water in plants
• plants have roots anchored in soil where they absorb water, but the leaves are uplifted and exposed to solar energy. A plant contains a sytem of vessels that reaches from the roots to the leaves, so water evaporating from the leaves is immediately replaced with water molecules from the vessels. Because water molecules are cohesive, a tension is created that pulls water up from the roots. Adhesion of water to the walls of the vessels also helps prevent the water column from breaking apart
  
• unlike most substances, frozen water is less dense than liquid water
• as water cools, the molecules come closer together (densest at 4°C)
• at temperatures below 4°C there is only vibrational movement, and hydrogen bonding becomes more rigid but also more open, so water expands as it freezes and is less dense)
• bodies of water freeze from the top, acting as an insulator to protect water underneath and making life possible instead of accumulating at the bottom of lakes and oceans
• hydrogen ions (H⁺)
• hydroxide ions (OH^-)
• H-O-H ↔ H⁺ + OH^-
• only a few water molecules at a time are dissociated, and the actual number of these ions is very small (10^-7 moles/liter)
• acids-molecules that dissociate in water, releasing hydrogen ions (H⁺)/higher concentration
  
• strong acids dissociate almost completely, strong bases dissociate almost completely
• bases-molecules that either take up hydrogen ions (H⁺) or release hydroxide ions (OH^-)/higher concentration
  
• pH scale-indicates acidity and basicity (alkalinity) of a solution
  
• ranges from 0 to 14
• logarithmic as opposed to exponential
• devised to simplify discussion of the hydrogen ion concentration [H⁺] and hyroxide ion concentration [OH^-] by eliminating th use of cumbersome numbers
• each pH has 10 times the amount of hydrogen ions as the next higher unit
• 7 is neutral pH, pure water has an equal number of hydrogen and hydroxide ions
• source: one mole of pure water contains only 10^-7 moles/liter of hydrogen ions
• in living things pH needs to be maintained within a narrow range or there are health consequences
• pH of our blood is always about 7.4, slightly basic
• buffers-most important of mechanisms to prevent pH changes; keep pH within normal limits because they are chemicals or combinations of chemicals that take up excess hydrogen or hydroxide ions
• blood always contains a combination of some carobic acid and some bicarbonate ions, so in case:
  H⁺ + HCO₃^- → H₂CO₃, then
  OH^- + H₂CO₃ → HCO₃^- + H₂O
• these reactions prevent any significant change in blood pH
  

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Lecture Notes 8/31-9/21

• characteristics of life
• life shows organization-cell theory
• life acquires nutrients for survival-photosynthesis/respiration
• life uses energy to maintain organization-homeostasis
• life respons to its environment-adaptation/evolution
• life needs to reproduce to maintain itself through time
• nutrients: water, minerals (Na, K, Ca, Mg, Fe, Cu, Zn, etc.), vitamins, hydrocarbon molecules that are C-, H- based (carbohydrates, proteins, lipids/fats)
• methodology to learn about the natural world
1. identify a problem to study-natural curiousity
2. examine the literature to find out what is already known
3. formulate a hypothesis to test to learn new information
4. design and run an experiment to test the hypothesis
5. collect observations and measurements (data)
6. analyze and interpret your observations and measurements
7. draw a conclusion about the truthfulness of the hypothesis
   
• supernatural-religion, cannot be tested
  
• pure research-no practical applications, just "because it's there"
• applied research-business, commerical exploitation, practical use
• evolution-
• descent with modification through time (paleontology def.)
• change through time such that one species changes into one or more new species
• active form, it's still occurring but extremely slow
  
• descent through many generations
• survival of the fittest (e.g. black pague, smallpox in North Africa, etc.)
• humans have existed for only a short amount of time, as opposed to cockroaches or the bristlecone pine
• Earth is about 4.5 billion years old
• mechanism: Darwin was influenced by Malthus theory on limiting factors
1. natural populations' reproductive capacity exceeds environment's capacity to support offspring
2. environment interacts with overproduction to "select" those best adapted which "survive"
3. those best adapted to environment survive
   
• sexual reproduction provides new combinations of existing genetic material upon which the environment interacts/has survived the environment
• most mutations are harmful
  
• Origin of Species was highly controversial
• continental/genetic drift is the driving force of evolution-a slow, steady movement over millions of years resulting in climatic changes which "selects" the "best adapted"
• times of bounty and scarcity, wintertime is harder so more "selection"
  
• fossils-first/oldest evidence of life, relatively rare as conditions must be perfect
• many fossils in Montana and southwestern America
• from fossils, you can divine their behaviour, what has happened in the geological past, and support evolution
• comparitive anatomy
• homology-same structure, different function (i.e. human arm, bird wing, whale flipper, horse leg)
• scales are the origin of teeth
• new genes are never created, they already exist just as different combinations of genes; there is a tremendous variety of traits
  
• recessive alleles appear only when there are no dominant traits
• start with the phenotype, then infer the genotype (begin with recessive)
• Hardy-Weinberg equilibrium is the mathematical proof of evolution

p² + 2pq + q² = 1
p + q = 1
q² = 16%
q = √.16 = .4
p + .4 = 1
p = .6
.6² + .4(.6) + .4² = 1
.36 + .48 + .16 = 1