Study list for HON1070 (Fall 2012) 1. Basic chemistry a.

Chemical properties of the major biologically-relevant elements: CHNOPS Electronegativity scale: H (2.1), C (2.5) S (2.7?) N (3.0) O (3.5) F(4.0) i. Valence the number of valence bonds a given atom has formed. The amount of possible bonds an atom can make or has made. H has a valence of one. O- two. this needs to be checked ii. Electronegativity how strongly an atom pulls an electron towards it. b. Types of chemical bonds and their properties, with examples i. Covalent electrons are shared. 1. Polar electrons spend most of their time closer to one atom. 2. Non-polar electrons are shared equally between atoms. ii. Non-covalent 1. Ionic between metal and non-metal. Electrons are transferred from one atom to the other, and the two charged atoms stick together through electrostatic forces. 2. Hydrogen bonds A bond between a Hydrogen atom that has a partially positive charge and another highly electronegative atom (that has a partially negative charge. Water forms hydrogen bonds with other water molecules. ) 3. Hydrophobic bonds (Van derWaals; Entropy minimization) Hydrophobic bonds are bonds are between non polar molecules; low water-soluble molecules. Low soluble molecules are generally non polar molecules with long carbon tails that do no t interact with water.

c. Van derWaals - In physical chemistry, the van der Waals force (or van der Waals interaction), named after Dutch scientist Johannes Diderik van der Waals, is the sum of the attractive or repulsive forces between molecules (or between parts of the same molecule) other than those due to covalent bonds, the hydrogen bonds, or the electrostatic interaction of ions with one another or with neutral molecules

2. Isotopes definition, use as tools isotopes are atoms with an additional or a lost neutron(s). 3. Organic Chemistry a. Molecular shapes Molecular shapes determine the way biological molecules interact with each other. For example An enzyme will only catalyze a specific reaction and no other reaction. A protein that responds to a signal molecule can only be activated by that specific molecule (or something very similar to that shape). b. Functional groups and their properties (Some page in the text book). Pg 64 4. Biochemistry a. Macromolecules monomers and basic structure (be able to recognize) i. Polysaccharides complex sugars, made up of two or more glucose molecules. (pg 71) 1. Sugars types and basic structure; ring structure in aqueous solution. Two different glucose molecules: alpha and beta glucose. 2. Glycosidic bonds There are alpha glucoses and beta glucoses that can form different structures depending on how the glucose molecules are bounded to one another. It is a covalent bond formed between two monosaccharides by a dehydration reaction. 3. Types of polysaccharides (cellulose, amylose) a polysaccharide is a substance of many monosaccharides linked together by glycosidic linkages. Cellulose (pg 72) is made up of glucose, but in glucose of two different forms (alpha and beta). Cellulose is a major component of the cell walls of plants it is indigestible to humans. (Bacteria in cows stomachs contain the enzyme that can break down the bonds of cellulose.) Amylose is a form of starch (a polysaccharide) that is made up of only alpha form glucose molecules. It is used as energy and can be found in plants. Animals have glucose polysaccharides too, but the one found in animals is called glycogen. ii. Lipids (pg 74) 1. Triglycerides and fatty acids glycerol is an alcohol. A fatty acid has a long carbon skeleton , usually 16-18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group, the functional group that gives these molecules the name fatty acid. The rest of the skeleton is a hydrocarbon chain. In making a fat, three fatty acid molecules are each joined by an ester linkage,

a bond between a hydroxyl group and a carboxyl group. The resulting fat, a triacylglycerol, consists of three fatty acids linked to one glycerol molecule. 2. Steroids (pg 77) are lipids characterized by a carbon skeleton consisting of four fused rings. Different steroids, such as cholesterol and the vertebrate sex hormones, are distinguished by the particular chemical groups attached to the rings. 3. Phospholipids (pg76) A polar (hydrophilic head) made of a phosphate group between a glycerol and a choline molecule. The molecule is a fatty acid with two hydrocarbon tails, with the phosphate group with the attached choline attached to the glycerol end of the fatty acid. The hydrocarbon tail is non-polar (hydrophobic). iii. Nucleic acids Made of a phosphate, a sugar and a nitrogenous base. There are 5 different nucleic acids. (pg 87) 1. Monomer structures (memorize) the 5 monomers are: adenine and guanine which are purines (2 rings) and thymine, cytosine and uracil which are pyrimidines (1 ring). 2. Differences and similarities between DNA and RNA DNA uses Adenine and Thymine pairs and Guanine and Cytosine pairs, while RNA uses Uracil instead of Thymine. iv. Proteins 1. Amino acids structures and properties (memorize) Are the building blocks of polypeptides which form proteins. 2. Levels of 3-dimensional structure a. Primary linear sequence of amino acids. b. Secondary a-helix & b-pleated sheet made up of the molecular interactions between amino acids. Formed through hydrogen bonds. c. Tertiary contribution of amino acid functional groups The overall structure of the polypeptide; it is formed through interactions of alpha helix and beta pleated sheets. d. Quaternary the interaction of multiple polypeptides to form a protein. 3. Denaturation and renaturation When an enzyme is moved to an area of PH that it doesnt normally function in, or a temperature that it doesnt normally function in, the enzyme can unfold and be

inactive. It has been denatured. By placing the enzyme back in its original environment, or by removing that which is causing it to be denatured, it is possible for the enzyme to resume native shape. There are permanent denaturing substances (molecules) that bind to enzymes causing them to permanently change shape. Those enzymes cannot be renatured.

a. Anfinsen experiment the experiment on protein folding. Renaturing RNase and then testing to see if activity returned to the enzyme. The more time we allowed for the enzyme to return to activity, the greater its activity was. After a certain amount of time, the enzyme would have been able to hydrolyze so much product that the product would inhibit its activity, causing a lower percentage than previous samples (see XL graph in bio lab folder).

b. Sickle cell anemia: molecular mechanism. Sickle cell is the replacement of one amino acid in a hemoglobin molecuse polypeptide sequence by another, a valine replacing a glutamic acid. (pg84) With this substitution, a hydrophobic region of the cell is to the outside instead of the inside. Normal red blood cells are disk-shaped, but in sickle-cell disease, the abnormal hemoglobin molecules tend to crystallize, deforming some of the cells into a sickle shape.

c. Degradation Proteasome, ubiquitin, ubiquitin ligases Proteasomes are protein complexes inside all eukaryotes and archaea, and in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm.[1] The main function of the proteasome is to degrade unneeded or damaged proteins by

proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that carry out such reactions are called proteases. Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins. The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into amino acids and used in synthesizing new proteins.[2] Proteins are tagged for degradation with a small protein called ubiquitin. The tagging reaction is catalyzed by enzymes called ubiquitin ligases. Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein.[2]

Ubiquitin - Ubiquitin is a small regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic organisms. It directs proteins to compartments in the cell, including the proteasome which destroys and recycles proteins. Ubiquitin can be attached to proteins and

label them for destruction.

Ubiquitin ligases - A ubiquitin ligase (also called an E3 ubiquitin ligase) is a protein that in combination with an E2 ubiquitin-conjugating enzyme causes the attachment of ubiquitin to a lysine on a target protein via an isopeptide bond; the E3 ubiquitin ligase targets specific protein substrates for degradation by the proteasome. In general, the ubiquitin ligase is involved in polyubiquitination: A second ubiquitin is attached to the first, a third is attached to the second, and so forth. Polyubiquitination marks proteins for degradation by the proteasome. However, there are some ubiquitination events that are limited to mono-ubiquitination, in which only a single ubiquitin is added by the ubiquitin ligase to a substrate molecule. Mono-ubiquitinated proteins are not targeted to the proteasome for degradation, but may instead be altered in their cellular location or function, for example, via binding other proteins that have domains capable of binding ubiquitin

d. Prions and their associated diseases 5. A prion - is an infectious agent composed of protein in a misfolded form.[2] This is the central idea of the Prion Hypothesis, which remains debated.[3] This would be in contrast to all other known infectious agents (virus/bacteria/fungus/parasite) which must contain nucleic acids (either DNA, RNA, or both). The word prion, coined in 1982 by Stanley B. Prusiner, is derived from the words protein and infection.[4] Prions are responsible for the transmissible spongiform encephalopathies in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle and CreutzfeldtJakob disease (CJD) in humans. All known prion diseases affect the structure of the brain or other neural tissue and all are currently untreatable and universally fatal.[5] Prions cause other prteins to miss-fold.

a. Enzymes i. Basis of catalysis - Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself Enzymes are the things which catalyze reactions. They are shaped to help specific reactions occur, and no other. Enzymes are proteins made up of one or more polypeptides. (A strand of RNA can also function as an enzyme). Enzymes have specific shapes that allow specific molecules to enter the binding-site. At the binding-site, the bonds of the substrates are stressed, lowering the activation energy required for the reaction between the two reactants to occur. Enzymes may not be reuired to cause a reaction occur, but they can greatly cause a reaction to speed up. For example, one can make a reaction that on its own would not show any appreciable change, even over many years, but with an enzyme present, the reaction may take place in minutes. ii. Equilibrium and reversibility of chemical reactions Equilibrium is when the reactants and the products of a reaction are proportionally balanced (The actual amount of substances does not have to be equal). In equilibrium, there is no net change of product of reactant. iii. Thermodynamics The study of the energy transformations that occur in a collection of matter. (pg144-145)

1. Go, DS : definition and importance G Free-energy change. (pg146) Free energy is the portion of a systems energy that can perform work when the temperature and pressure are uniform throughout the system, as in a living cell. The change in free energy, G = H -TS. This equation uses only properties of the system (the reaction) itself: H symbolizes the change in the systems enthalpy (in biological systems, equivalent to total energy); S is the change in the systems entropy; and T is the absolute temperature in Kelvin (K) units (K=C + 273) 2. Exergonic vs. Endergonic reactions Exergonic Reactions An exergonic reaction proceeds with a net release of free energy. Because the chemical mixture loses free energy (G decreases), is negative for an exergonic reaction. Using G as a standard for spontaneity, exergonic reactions are those that occur spontaneously. (Remember, the word spontaneous implies that it is energetically favorable, not that it will occur rapidly). Endergonic Reaction is one that absorbs free energy from its surroundings. Because this kind of reaction essentially stores free energy in molecules (G increases), G is positive. Such reactions are nonspontaneous, and the magnitude of G is the quantity of energy required to drive the reaction. If a chemical process is Exergonic (downhill), releasing energy in one direction, then the reverse process must be Endergonic (uphill), using energy. A reversible process cannot be downhill in both directions. If G = -686 kcal/mol for respiration, which converts glucose and oxygen to carbon dioxide and water, then the reverse process the conversion of carbon dioxide and water to glucose and oxygen must be strongly Endergonic, with G = +686 kcal/mol. Such a reaction would never happen by itself. iv. Active site (pg 154) Only a restricted region of the enzyme molecule actually binds to the substrate. This region, called the active site, is typically a pocket or groove on the surface of the enzyme where catalysis v. Catalytic cycle in chemistry is a term for a multistep reaction mechanism that involves a catalyst. The catalytic cycle is the main method for describing the role of catalysts in biochemistry, organometallic chemistry, materials science, etc. Often such cycles show the conversion of a precatalyst to the catalyst. Since catalysts are regenerated, catalytic cycles are usually written as a sequence of chemical reactions in the form of a loop. In such loops, the initial step entails binding of one or more reactants by the catalys, and the final step is the release of the product and regeneration of the catalyst.

vi. Regulation by inhibitors structural basis 1. Competitive something that is similar in shape to the reactanct, therefore able to bind at the binding site, preventing the desired substrate from entering the active site, and thereby slowing down the rate of the reaction. 2. Non-competitive allosterically (bind to a site other than the active site) bind to the enzyme, changing its shape and keeping it from performing its function. These molecules can bind reversibly or permanently.

6. Energy metabolism a. ATP (memorize structure) (pg 149) b. Glycolysis (know: hexokinase, pyruvate, NAD+/NADH, substrate-level phosphorylation, ATP requirement and yield, input-output, location in cell) sugar splitting. Glucose, a sic-carbon sugar, is split into two three-carbon sugars. These smaller sugars are the oxidized and their remaining atoms rearranged to form fwo molecules of pyruvate. Hexokinase - An enzyme that transfers a phosphate group from ATP to glucose, making it more chemically reactive. The charge on the phosphate also traps the sugar in the cell. Pyruvate The beginning of their formation begins when glucose molecule is cut into two 3 carbon sugars. These smaller sugars are then oxidized and their remaining atoms rearranged to form two molecules of pyruvate. c. TCA cycle (know roles of: oxaloacetic acid, citric acid, Acetyl CoA, input-output, cellular location) Krebs cycle (in mitochondrial matrix) d. Pyruvate has to go into mitochondria. When Pyurvate is becoming acetal CoA you get one NADH in intermediate step per pyruvate. (one glucose molecule produces two pyruvate). Each acetyl coA goes into the cirtic acid cycle. In the citric acid cycle you get 3NADH one FADH and two CO2. You also get a CO2 in the process that makes Acetyl CoA so 3CO2 are produced all together. (pg 170)

e. Oxidative phosphorylation

i. Cell location - is a metabolic pathway that uses energy released

by the oxidation of nutrients to produce adenosine triphosphate (ATP). Although the many forms of life on earth use a range of different nutrients, almost all aerobic organisms carry out oxidative phosphorylation to produce ATP, the molecule that supplies energy to metabolism. This pathway is probably so pervasive because it is a highly efficient way of releasing energy, compared to alternative fermentation processes such as anaerobic glycolysis.
The electron transport chain in the mitochondrion is the site of oxidative phosphorylations in eukaryotes. ii. Electron transport and cytochromes An electron transport chain couples electron transfer between an electron donor (such as NADH) and an electron acceptor (such as O2) with the transfer of H+ ions (protons) across a membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of adenosine triphosphate (ATP). Electron transport chains are the cellular mechanisms used for extracting energy from sunlight in photosynthesis and also from redox reactions, such as the oxidation of sugars (respiration). Cytochromes are, in general, membrane-bound hemoproteins that contain heme groups and carry out electron transport. They are found either as monomeric proteins (e.g., cytochrome c) or as subunits of bigger enzymatic complexes that catalyze redox reactions. iii. Electrogenic pump & proton gradient The sodium-potassium pump is an example of en electrogenic pump, because it pumps unequal quantities of Na+ and K+ across the membrane; 3Na+ out of and 2K+ into the cell per pump cycle. In other words, it generates electricity by producing a net movement of positive charge out of the cell. Proton gradient An electrochemical gradient is a gradient of electrochemical potential, usually for an ion that can move across a membrane. The gradient consists of two parts, the electrical potential and a difference in the chemical concentration across a membrane. The difference of electrochemical potentials can be interpreted as a type of potential energy available for work in a cell. The energy is stored in the form of chemical potential, which accounts for an ions concentration

gradient across a cell membrane, and electrostatic energy, which accounts for an ions tendency to move under the influence of the transmembrane potential.

iv. Input and output essentially glucose is put in, CO2 and H2) are put out. v. ATP synthase & how it works

f. Fermentation why and how? Why: cells do it in the absence of energy. Cells only perform the glycolysis part of cellular respiration.

7. Cell structure and Function a. Cytoskeleton, especially structure and function of microtubules Microtubules shape the cell, guide organelle movement, and separate chromosomes in dividing cells. Cilia and flagella are motile appendages containing microtubules. Primary cilia also play sensory and signaling roles. Microfilaments are thin rods functioning in muscle contraction, amoeboid movement, cytoplasmic streaming, and microvillus support. Intermediate filaments support cell shape and fix organelles in place.

b. Organelles i. Nucleus, nucleolus Is surrounded by nuclear envelope (double membrane) perforated by nuclear pores; nuclear envelope is continuous with endoplasmic reticulum. The nucleus houses chromosomes, which are made of chromatin (DNA and proteins); contains nucleoli, where ribosomal subunits are made; pores regulate entry and exit of materials. Nucleolus a small dense spherical structure in the nucleus of a cell during interphase.

ii. Endoplasmic reticulum (rough, smooth) An extensive network of membrane-bounded tubules and sacs; membrane separates lumen from cytosol; continuous with nuclear envelope. Smooth ER: synthesis of

lipids, metabolism of carbohydrates, Ca2+ storage, detoxification of drugs and poisons (The liver is made of cells that have a lot of smooth ER). Rough ER: aids in synthesis of secretory and other proteins from bounds ribosomes; adds carbohydrate to protein to make glycoproteins; produces new membrane.

iii. Golgi Stacks of flattened membranous sacs; has polarity (cis and trans faces). Modification of proteins, carbohydrates on proteins, and phospholipids; synthesis of many polysaccharides; sorting of golgi products, which are then released in vesicles.

iv. Peroxisomes Specialized metabolic compartment bounded by a single membrane. Contains enzymes that transfer hydrogen atoms from substrates to oxygen, producing hydrogen peroxide (H2O2) as a byproduct; H2O2 is converted to water by another enzyme.

v. Chloroplasts Typically two membranes around fkuid stroma, which contains thylakoids stacked into grana (in cells of photosynthetic eukaryotes, including plants). Performs photoynthesis.

vi. Mitochondria Bounded by double membrane; inner membrane has infoldings (cristae). Site in an animal cell where cellular respiration takes place. Mitochondria can be found in plant cells too 1. Structure Both are double membranes. 2. Evolutionary origin (evidence) It is believed that Mitochondria were once bacteria that lived on their own, and that they merged with other cells to form eukaryotic cells that exist today. This is the endosymbiotic theory; the evidence for this is riquetzzia. (LOOK UP) Cellular Respiration (Saras notes)

3 Stages

1. Glycolysis 2. Krebs cycle 3. Oxidative phosphorylations.

A. Glycolysis There are ten steps. Substrate level phosphorylation is used to form ATP. Gain: 2 pyruvates, 2 ATP, 2NADH, 2H2O. B. Krebs Cycle Before the krebs cycle occurs, pyruvate is oxidized o acetyl CoA; this occurs when the pyruvate enters the mitochondria. The acetyl CoA joins with the oxaloacetate to begin the process. Substrate level phophorylation is again used here to create ATP. (used Saras notes for the rest of this because I decided it was useless to continue to type her notes.) vii. Cilia and flagella A specialized arrangement of microtubules makes up cilia and flagella. Flagella usually undulate (the way they move) think sperm. Cilia have a back and forth motion. Cells would usually have one flagellum, or many cilia.

c. Differences and similarities between Prokaryotes and Eukaryotes Prokaryotes are single celled organisms. No membrane bound organelles or DNA. In some bacteria (I dont know if all) DNA is circular (ex. E. Coli). Prokaryotes are smaller than eukaryotes. Eukaryotes Large. Have membrane bound organelles/nucleus. d. Biological Membranes Lipid bilayer made of phospholipids. Cholesterol is a steroid that stabilizes the lipid bilayer. Temperature affects the fluidity of the membrane. Colder less fluid, warmer more fluid. Too fluid or too slow are both bad. Fluid mosaic structure and properties - The plasma membrane is described to be fluid because of its hydrophobic integral components such as lipids and membrane proteins that move laterally or sideways throughout the membrane. That means the membrane is not solid, but more like a 'fluid'. (pg125) In the fluid mosaic moel, the membrane is a fluid structure with a mosaic of various proteins embedded in or attached

to a double layer (bilayer) of phospholipids. The membrane is depicted as mosaic because like a mosaic that is made up of many different parts the plasma membrane is composed of different kinds of macromolecules, such as integral proteins, peripheral proteins, glycoproteins, phospholipids, glycolipids, and in some cases cholesterol, lipoproteins. i. According to the model, the plasma membrane is a lipid bilayer (interspersed with proteins). It is so because of its phospholipid component that can fold in itself creating a double layer - or bilayer - when placed in a polar surrounding, like water. This structural feature of the membrane is essential to its functions, such as cellular transport and cell recognition. 1. Phospholipid distribution inner and outer leaflets 2. flippase - are a family of transmembrane lipid

transporter enzymes located in the membrane responsible for aiding the movement of phospholipid molecules between the two leaflets that compose a cell's membrane (transverse diffusion). Their existence was predicted in 1972 by Mark Bretscher, who also named them, to explain how an asymmetric phospholipid bilayer could be formed.[1] Although phospholipids diffuse rapidly in the plane of the membrane, their polar head groups cannot pass easily through the hydrophobic center of the bilayer, limiting their diffusion in this dimension. Phospholipid molecules that are synthesized in the cell are incorporated into the cytoplasmic face of the membrane, where flippases can transfer them to the exoplasmic face. Energy-dependent flippases require energy input in the form of ATP to carry out their function, often known as a flip-flop. However, there are energy-independent flippases that do not require the hydrolysis of ATP and are unidirectional in their action. These energy-independent flippases are responsible for transferring newly sythesised lipids from the outer to the inner leaflet of membranes.

ii. Transmembrane proteins - is a protein that goes from one side of

a membrane through to the other side of the membrane. Many TPs function as gateways or "loading docks" to deny or permit the transport of specific substances across the biological membrane, to get into the cell, or out of the cell as in the case of waste byproducts. As a response to the shape of certain molecules these "freight handling" TPs may have special ways of folding up or bending that will move a substance through the biological membrane.
There are two types of transmembrane proteins:

8. Alpha-helical. These proteins are present in the inner membranes of bacterial cells or the plasma membrane of eukaryotes, and sometimes in the outer membranes.[3] This is the major category of transmembrane proteins. In humans, 27% of all proteins have been estimated to be alphahelical membrane proteins.[4] Beta-barrels. These proteins are so far found only in outer membranes of Gram-negative bacteria, cell wall of Grampositive bacteria, and outer membranes of mitochondria and chloroplasts. All beta-barrel transmembrane proteins have simplest up-and-down topology, which may reflect their common evolutionary origin and similar folding mechanism.
1. Amphipathic helices - High

amphiphilicity is a hallmark of interfacial helices in membrane proteins and membrane-active peptides, such as toxins and antimicrobial peptides. Although there is general agreement that amphiphilicity is important for membrane-interface binding, an unanswered question is its importance relative to simple hydrophobicity-driven partitioning. We have examined this fundamental question using measurements of the interfacial partitioning of a family of seventeen-residue amidated-acetylated peptides into both neutral and anionic lipid vesicles. Composed only of Ala,

Leu, and Gln residues, the amino acid sequences of the peptides were varied to change peptide amphiphilicity without changing total hydrophobicity. We found that peptide helicity in water and interface increased linearly with hydrophobic moment, as did the favorable peptide partitioning free energy. This observation provides simple tools for designing amphipathic helical peptides. Finally, our results show that helical amphiphilicity is far more important for interfacial binding than simple hydrophobicity.

2. Lateral movement & lipid rafts lateral movement phospholipids can move from side to side within the membrane. Proteins can be free-moving throughout the membrane of can be anchored in place. 3. Functions a. Transport non-polar molecules have an easy time diffusing across the plasma membrane, where as polar molecules diffuse slowly across the membrane. Membranes display selective permeability allowing some (non-polar) substances an easier time moving across the membrane than others (polar). i. Active transport symport, antiport, Na-K ATPase Symport an integral membrane protein that is involved in movement of two or more different molecules or ions across a phospholipid membrane such as the plasma membrane in the same direction, and is, therefore, a type of co transporter. Typically, the ion(s) will move down the electrochemical gradient, allowing the other molecule(s) to move against the concentration gradient. The movement of the ion(s) across the membrane is facilitated diffusion, there may be several molecules transported of each type. Antiport An antiporter is an integral membrane protein involved in secondary active transport of two or more different molecules or ions across a phospholipid membrane such as the plasma membrane in opposite directions. In secondary active transport, one species of solute moves

along its electrochemical gradient, allowing a different species to move against its own electrochemical gradient. This movement is in contrast to primary active transport, in which all solutes are moved against their concentration gradients, fueled by ATP. Transport may involve one or more of each type of solute. For example, the Na+/Ca2+ exchanger, used by many cells to remove cytoplasmic calcium, exchanges one calcium ion for three sodium ions. ii. Facilitated diffusion is a process of passive transport (as opposed to active transport), with this passive transport aided by integral membrane proteins. Facilitated diffusion is the spontaneous passage of molecules or ions across a biological membrane passing through specific transmembrane integral proteins. aquaporin aquaporins are special channels in the cell membrane that facilitate the movement of water across the cells membrane. Are proteins embedded in the cell membrane that regulate the flow of water. Aquaporins are integral membrane proteins from a larger family of major intrinsic proteins that form pores in the membrane of biological cells. Integral protein permanently attached to the plasma membrane.

Major intrinsic proteins are a large family of transmembrane protein channels that are grouped together on the basis of sequence similarities. b. Signaling (receptors) Receptors on the cells surface (like a receptor tyrosine kinase) will be activated when the proper ligand interacts with the binding site. c. Cellular adhesion oligosaccharides act as recognition tags on the surface of cells. They act as glue to adhere cells together; this helps provide uniformity. This helps in tissue identity, and protein sorting and targeting within cells; kind of like a postal code.

9. What Is Atherosclerosis?

10. Atherosclerosis is hardening and narrowing of medium-size and

larger blood vessels, such as the aorta and those found in the heart (coronary arteries), brain, and legs. Atherosclerosis is by far the most common type of hardening of the arteries. It is caused by the slow buildup of plaque on the inside walls of arteries. Plaque is made up of fat, cholesterol, calcium, and other substances found in your blood. As it grows, the buildup of plaque narrows the inside of the artery and, in time, may restrict blood flow.

11. Cell signaling a. Basis of Ligand-receptor interaction and specificity b. Types of receptors and examples: i. G-protein-linked (G protein mechanism) ii. Tyrosine kinases iii. Ligand-gated ion channels iv. Steroid receptors v. 2nd messengers 1. cAMP and adenyl cyclase both act as secondary messengers. 2. IP3 and Ca2+ - both can cause cellular responses when released in a cell.

Second messengers are small non-protein molecules that act as intermediaries in signal transmission. Two important second messengers are cyclic AMP and calcium ions. Phospholipase C cleaves IP3 from a membrane protein, and IP3 then binds to a calcium channel on the ER. Adenylyl cyclase makes cAMP which then phosphorylates other proteins in the chain.
c. Signal transduction - occurs when an extracellular signaling[1] molecule

activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response

i. Phosphorylation cascades - is a sequence of events where one

enzyme phosphorylates another, causing a chain reaction leading to the phosphorylation of thousands of proteins. Receptor proteins (located in the plasma membrane or inside the cell) bind signaling molecules. The reception of the signal causes a shape change in the receptor molecule, to which other molecules inside the cell respond. The message is then relayed through signal transduction, which may involve a phosphorylation cascade or second messengers such as cAMP, Ca2+, or IP3. Possible responses to the signal may include synthesis of a particular protein or regulation of a particular enzyme.

ii. Nuclear targets the final proteins that are meant to be activated, found in nucleus. d. Protein kinases (esp. tyrosine & serine/threonine) Phosphorylate specific proteins in the beginning of transduction pathway. This begins when a ligand binds to a receptor protein. This causes a confirmational change that causes the GDP attached to the inactive form of a G-protein to be change for a GTP, causing the protein to enter its active form. This then begins a phosphorylations cascade, causing proteins in the chain to be phosphorylated in order to transfer the message from the signal molecule at the cells surface to whatever the intended target may be. (chpt 11)

e. Quorum-sensing in bacteria - is a system of stimulus and response

correlated to population density. Many species of bacteria use quorum sensing to coordinate gene expression according to the density of their local population

f. Signaling disruption and cancer 12. Mitosis the process by which a cell replicates.

a. Why and how? Names of recognized phases the cell gets too big and sow in order to survive divides. b. Chromosomes, chromatids, centromere, centriole, spindle, kinesin motors chromosomes condensed DNA that has genes on it. Chromatids sister chromatids are held together at the centromere during replication. They are split during the teleophase. Centriole - Centrioles are involved in the

organization of the mitotic spindle and in the completion of cytokinesis.[9] Centrioles were previously thought to be required for the formation of a mitotic spindle in animal cells. However, more recent experiments have demonstrated that cells whose centrioles have been removed via laser ablation can still progress through the G1 stage of interphase before centrioles can be synthesized later in a de novo fashion.[10] Additionally, mutant flies lacking centrioles develop normally, although the adult flies lack flagella and cilia.[11]
Spindle pushes the two nucleus apart in order to allow the cell to divide. Kinesin motor - A kinesin is a protein belonging to a class of motor

proteins found in eukaryotic cells. Kinesins move along microtubule filaments, and are powered by the hydrolysis of ATP (thus kinesins are ATPases). The active movement of kinesins supports several cellular functions including mitosis, meiosis and transport of cellular cargo, such as in axonal transport. Most kinesins walk towards the plus end of a microtubule, which, in most cells, entails transporting cargo from the centre of the cell towards the periphery. This form of transport is known as anterograde transport.

13. Cell cycle a. Recognized phases (M, G1, S, G2; G0). What happens in each. M phase is mitosis cell division. G1 is the first part of interphase, cell growth occurs during this phase. S DNA is replicated during this phase (S for synthesis DNA synthesis). G2 second part of interphase, more growing. G0 cells that arent dividing/that dont divide at all are in this phase (nerve cells and muscle cells). b. Check points (where and why? Tumor suppressors as cell cycle inhibitors) There are three major check points: found at G1, G2 and M phases. The G1

seems to be the most important. If a cell receives the go-ahead at G1, it will usually complete G1, S, G2 and M phases. c. MPF, cyclins and cyclin-dependent protein kinases d. Role of oncogenic mutations 14. Genetics a. Meiosis why and how? Meiosis allows for the reproduction of a new organism, not just a cell. Its like meiosis only twice. A cell duplicates its chromsomes, but differently then when just dividing. Homologus chromosomes line up and lock together. For ex: chromosome 1 from Dad lines up with 1 from Mom (after each chromosome has been duplicated [sister chromatids stay together]) and the two are locked together. This is called a tetrad (4 2 from Dad and 2 from Mom locked together) the pairs will be divided twice. In one cell from the first division, you can have a pair of Dads from 1, but a pair of Moms from 2. (Pieces of Moms and Dads can switch through recombination. Each tetrad is attached to a spindle and pulled to the center; the homologus pairs are then pulled apart. (homologus pairs have been separated) the cell divides and now you have two daughter cells each with 23 DOUBLE STRANDED chromosomes. These two daughter cells will divide (this is called meiosis 2 the first division is meiosis one) the same thing happens chromosomes are lined up in spindle, and sister chromatids are separated. In the end we have four cells each with 23 chromosomes INSTEAD of 23 PAIRS. i. Synapsis and crossing-over; recombinant genotypes ii. Diploid vs haploid, zygote, gamete iii. b. Mendelian inheritance i. Gene (trait), allele, phenotype vs genotype ii. Dominant vs Recessive: genetic definition, molecular definition iii. Parental, F1, F2 generations iv. Homozygous vs heterozygous v. Test cross vi. Punnet square vii. Mendels laws of segregation, independent assortment viii. Incomplete dominance, multi-allelic vs multi-gene inheritance ix. Sex-linked inheritance x. Karyotype; chromosomal non-disjunction and its consequences c. Molecular Genetics i. Basic experiments establishing DNA as the genetic material 1. Griffeth; Avery, McLeod & McCarty

2. Hershey & Chase ii. Double helix and base pairs (memorize structures and positions of the hydrogen bonds) 1. Chargaffs rules 2. Watson & Crick model antiparallel strands iii. DNA replication 1. Meselsen & Stahl experiment 2. Leading vs lagging strand 3. The replisome: roles of proteins/enzymes a. Primers and primase b. Helicase, DNA polymerases, ligase, topoisomerase, singlestranded DNA-binding proteins c. Telomeres and telomerase iv. Response to DNA damage 1. Repair (e.g. thymine dimer excision) 2. Mutation and its relationship to repair 3. Cell cycle arrest 15. Accessing genetic information a. Transcription i. RNA polymerases (3 in Eukaryotes, 1 in prokaryotes) ii. Regulatory sequences associated with genes: promoters vs terminators iii. Initiation complex b. Post transcriptional RNA processing i. 5capping, polyadenylation ii. Splicing and the spliceazome: introns, exons, lariats and SnRNPs iii. mRNA vs primary transcript c. Translation i. The genetic code (memorize the three stop codons and the codons for methionine and one other amino acid of your own choice) ii. tRNA & aminoacyl-tRNA-aynthases iii. Ribosome and the role of structural RNA 16. Regulation of Gene activity a. In prokaryotes: the operon (operators, repressors & co-repressors/inducers, activators) i. Lac operon: induction ii. Trp operon: repression

iii. Catabolite repression concept of additional regulatory proteins to integrate different signals b. In eukaryotes: basal promoter vs enhancer sequences i. Sequence-specific DNA binding proteins ii. The transcriptasome c. Multiplex analysis of gene expression: the microarray and individualized medicine.

Some Basic Concepts Importance of 3-dimensional structure of macromolecules Molecular machines Carrier molecules in metabolism Electrons as carriers of energy Metabolic pathways Cell organization - compartmentalization

Good reading, but not on final exam this year 17. Microbial models for molecular genetics a. Bacteria useful as simple cells b. Viruses analogy to flash drive (cell has the OS, virus has a case, information, and a way to attach to the computer circuitry) i. Structure of capsid 1. Simple icosahedral, helical (examples) 2. Composite T-even bacteriophage (stepwise assembly via a genetic program) 3. Enveloped lipid blayer membrane derived from host cell + viral glycoproteins ii. Nucleic acid DNA or RNA, circular or linear, single or double-stranded, one chromosome or multiple chromosomes iii. Host cell specificity provided by physical attachment to receptors on cell surface iv. Mode of replication lytic vs. lysogenic v. HIV life cycle as it reflect all of the above; reverse transcriptase 18. Recombinant DNA a. Restriction endonucleases, vector, clone, host b. DNA sequencing

c. PCR Semi-autonomous organelles and evolutionary symbiosis Apoptosis and programmed cell death