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Isotopes: Isotopes are atoms with the same number of protons but differ in number of neutrons; e.g., a carbon atom has six protons but may have more or less than usual six neutrons Valence Shell: Outer shell of an atom. Atoms with few electrons in their valence shell tend to have more free electrons since these valence electrons are more loosely bound to the nucleus. Ionic Bonds: Ionic bonds form when electrons are transferred from one atom to another. Losing or gaining electrons, atoms participating in ionic reactions fill outer shells, and are more stable. Covalent Bonds: Covalent bonds result when two atoms share electrons so each atom has octet of electrons in the outer shell. . Structural formulas represent shared atom as a line between two atoms; e.g., single covalent bond (H-H), double covalent bond (O=O)Three dimensional shape of molecules is not represented by structural formulas but shape is critical in understanding the biological action of molecules: action of insulin, HIV receptors, etc. Hydrogen Bond forms between… › slightly positive hydrogen atom of one molecule and slightly negative atom in another or the same molecule. pH is a measure of… › How acidic or basic a solution is. Acidic Solution has more H+ ions Basic Solution has more –OH ions Buffer is › keep pH steady and within normal limits in living organisms.. Isomer is… › Are molecules or molecular compounds that are similar in that they have the same molecular formula, however have different arrangements of the atoms or groups of atoms (functional groups) involved. › Example: Fructose and glucose (C6H12O6) – same molecular formula but different arrangements › -OH – › C=O › -COOH › -NH2 › -SH › -OPO3 Hydroxyl Carbonyl Carboxyl Amino group Sulfhydryl group Phosphate group Hydrolysis Reaction › Reaction that breaks down compounds by the addition of H2O Dehydration synthesis reaction › Reaction in which two compounds are brought together with H2O released as a product Endergonic reaction › A reaction that requires the input of energy to occur A+B+energy C Exergonic reaction › A reaction that gives off energy as a product A+BEnergy +C Redox reaction › A reaction involving the transfer of electrongs General formula for monosaccharides are CnH2nOn Example: C6H12O6 (Glucose) Simple Sugar › Function: Sugar found in Nucleic Acid › Glucose: Sugar for the body › ATP: Cell Energy Polysaccharides: Carbohydrate containing 3 or more monosaccharides Storage form of energy Structural material in and around cells Difference between › Glycogen: Glucose molecules linked together (animal energy storage) › Starch: Glucose linked together (Plants energy storage) › Cellulose: composed of glucose molecules – formation of cell walls › Chitin: Glucose molecules joined togetherArthopods exoskeleton Structural Components of the following… › Fats: Lipids made by combining glycerol and three fatty acids. Used as long-term energy stores in cells › Phospholipids: is a lipid formed by combining a glycerol molecule with two fatty acids and a phosphate group; bilayered structure – component in cell membrane › Steroids: are lipids composed of four carbon rings that look like chicken wire. Examples: Cholesterol, sex hormones Cholesterol Testosterone Protein Chains: › Primary Structure: Sequence of amino acids to form a polypeptide chain (protein) › Secondary Structure: 3-D arrangement of a protein caused by hydrogen bonding at regular intervals along the polypeptide backbone › Tertiary Structure: 3-D arrangement of protein caused by interactions among the various R groups of the amino acids involved. › Quaternary structure: The arrangement of separate polypeptide “subunits” into a single protein Enzymes are proteins that act as organic catalyst (speed up reaction by lowering the energy (activation energy) needed for the reaction to take place but are not used up in the reaction. Induced-fit model: of enzyme-substrate interaction describes the active site of an enzyme as specific for a particular substrate that fits its shape. Allosteric enzyme: An allosteric enzyme is an enzyme that contains a region to which small, regulatory molecules ("effectors") may bind in addition to and separate from the substrate binding site and thereby affect the catalytic activity. On binding the effector, the catalytic activity of the enzyme towards the substrate may be enhanced, in which case the effector is an activator, or reduced, in which case it is a de-activator or inhibitor Four ways enzymes can be affected: › Temperature › pH › Concentration of the substrate › Concentration of the enzyme involved Prokaryotic: Simple cell › No nucleus Nucleoid : Genetic material › No membrane bond organelles Eukaryotic is more complex › Nucleus › Membrane bound organelles Ribosomes: protein synthesis Smooth ER: lipids synthesis, detoxification, and carbohydrate metabolism Rough ER: Ribosome are attached – proteins are produced Golgi apparatus: proteins, lipids, and other macromolecules sent to the Golgi to be modified by the addition of sugars and other molecules to form glycoproteins – products form vesicles Mitochondria: powerhouse—ATP is made here Lysosome: Digestion center Nucleus: Control center, contains DNA (genetic material) Vacuole: Storage (Plants have a larger structure) Chloroplast: Plants only – site for photosynthesis Fluid Mosaic Model: the membrane consist of a phospholipid bilayer with proteins of various lengths and sizes interspersed with cholesterol among the phospholipids. Two types of proteins in the cell membrane: › Integral proteins: implanted within the bilayer and can extend partway or all the way across the membrane › Peripheral proteins: such as receptor proteins, which are not implanted in the bilayer and are often attached to integral proteins of the membrane Difference between… › Diffusion: movement of molecules down their concentration gradient with the use of energy (area of higher concentration to lower concentration) › Osmosis: movement of water down its concentration gradient (passive diffusion). Going from a higher water concentration to area of lower water concentration › Active Transport: is the movement of a particle across a selectively permeable membrane against the concentration gradient (Going from low to high concentration) Hyperosmotic (Hypertonic): moving of water from a high solute in the environment to area of low solute concentration to environment. The water will move out of the cell 60% water 40% solute 40% water 60% solute Hypoosmotic (hypotonic): Is when the solute concentration is more in the cell than outside the cell. The water will move in of the cell 40% Water 60% Solute 60% water 40% solute Isosmotic (Isotonic): The solute and water is on the same on both sides 50% solute 50% water 50% solute 50% water Phases of Mitosis: › Prophase: Nuclear envelope disappears, chromatids appear, centrioles moves to poles › Metaphase: chromosomes move toward the center –Spindle are attached to the centromere › Anaphase: Chromatids separate and move toward the poles › Telophase: Chromatids move toward each poles, nuclear envelope reappears, cytokinesis begins Mitosis: is the dividing of body cells › Daughter cells will have the exact number chromosomes as the parent cells Meiosis : is the dividing of sex cells › Daughter cells will have half the number of chromosomes as the parent cells Cell cycle includes: › Interphase: the stage that prepares the cell for the cell division › Mitosis: is the division of the nucleus › Cytokinesis: division of the cytoplasm This is the way in which the cell has a type of check and balance system that ensures the cell is correct › › › › Checkpoints Density-dependent inhibition Growth Factors Cyclin and Protein kinases You may want to go back and look over this information Mitosis Meiosis Number of cells 2 diploid cells 4 haploid cells Crossing over No Yes-Prophase I Number of phases 1 (IPMATC) 2 (IPMATC & PMATC) No Interphase in the second phase Types of cells Body (Somatic) Cells Sex (Gamete) Cells Number of chromosomes Same number of chromosomes as the parent cell Diploid Different number of chromosomes as the parent cell Haploid Genetics Genetically Identical to the parent cell Genetically different to the parent cell The difference between meiosis I and meiosis II is that the cell does not go through interphase (Chromsome replication) during meiosis II. This will allow the cells to have half the number of chromsomes (haploid). Crossing over is when the homologous chromosomes match up during prophase I of meiosis, complementary pieces from the two homologous chromosomes wrap around each other and are exchanged between the chromosomes. Three parts to a nucleotide are…5 carbon sugar, phosphate, and nitrogen base › Serves as a puzzle piece to the nucleic acid strand (RNA or DNA) Adenine and guanine are purines Cytosine and Thymine are pyrimidine Base pairing states that Adenine will pair up with thymine and Cytosine will pair up with Guanine (Apple=Tart and Go=Cart) DNA replication occurs during the S-phase (interphase), semiconservative (which the one strands serves a template) Built in the 5’ to 3’ direction DNA helicase will unzip the strand by breaking the hydrogen bonds producing a replication fork Specific regions along DNA strand serve as primer sites that signal where replication should originate DNA polymerase – enzyme superstar binds to the primer site and adds nucleotides to the growing DNA chain (will only add to the 3’ end) The DNA polymerase only being used on the 3’ creates a problem which only allows the one strand to add nucleotides this is known as the leading strand. The other strand is known as the lagging strand The lagging strand consist of tiny pieces called Okazaki fragments, which are later connected by an enzyme called DNA ligase to produce the completed double stranded DNA molecule RNA primer allows for the RNA strand to bind to the DNA strand (this occurs during replication) DNA can only stay in the nucleus so it must send its instructions out to the cell. This is done by the second nucleic acid (RNA). Because DNA and RNA have very similar language it allows it to be accomplished. Transcription: is the process of taking DNA to a RNA strand (Occurs in the nucleus) › This is done by three steps: Initiation: When RNA polymerase attaches to the promoter region of a DNA strand Elongation: a promoter region recognition site that shows the polymerase where transcription will begin. Once RNA polymerase works by adding the appropriate RNA nucleotide to the 3’ of the growing strand Termination: tells the polymerase should conclude Translation: process by which the mRNA specified sequence of amino acids is lined up on a ribosome for protein synthesis (mRNA protein) Each amino acid carries a specific nucleotides/codes (codon) › Start Codon: AUG › Stop Codon: UAA, UAG, UGA Anticodon is the complementary to the codon (tRNA) that has been incorporated into the growing protein Define the following: › Promoter: a base sequence that signals the start site of genes transcription; this is where RNA polymerase binds to the begin the process › Operator: a short sequence near the promoter that assists in transcription by interacting with regulatory proteins › Operon: promoter/operator pair that services multiple genes Well known example is the lac operon › Repressor: protein that prevents the binding of RNA polymerase to the promoter site › Enhancer: DNA region also known as “regulator” that is located thousands of bases away frm the promoter › Inducer: a molecule that binds to and inactivates a repressor Structural Gene: one that specifies the amino acid sequence of a polypeptide chain Energy is… › The ability to do work Entropy is the measure of amount of energy that is not available for work ATP power cellular work the energy currency of cells (adenosine triphosphate) Functions: 1. CHEMICAL WORK - Supplies energy needed to make macromolecules that make up the cell (and organism) 2. TRANSPORT WORK - Supplies energy needed to pump substances across the cell membrane 3. MECHANICAL WORK - supplies energy needed to make muscles contract and other cellular parts to move (flagella) Glycolysis › a) a ten-step process that occurs in the cytoplasm b) converts each molecule of glucose to two molecules of pyruvic acid (a 3-carbon molecule) c) an anaerobic process - proceeds whether or not O2 is present ; O2 is not required d) net yield of 2 ATP per glucose molecule e) net yield of 2 NADH per glucose (NADH is nicotine adenine dinucleotide, a co-enzyme that serves as a carrier for H+ ions liberated as glucose is oxidized.) Kreb Cycle –occurs in the mitochondria › a) occurs in the inner mitochondrial matrix b) the acetyl group detaches from the coenzyme A and enters the reaction cycle c) an aerobic process; will proceed only in the presence of O2 d) net yield of 2 ATP per glucose molecule (per 2 acetyl CoA) e) net yield of 6 NADH and 2 FADH2 (FAD serves the same purpose as NAD) f) in this stage of cellular respiration, the oxidation of glucose to CO2 is completed › GO BACK AND LOOK AT YOUR CYCLE Electron Transport System – occurs in the mitochondria › a) consists of a series of enzymes on the inner mitochondrial membrane b) electrons are released from NADH and from FADH2 and as they are passed along the series of enzymes, they give up energy which is used to fuel a process called chemiosmosis by which H+ ions are actively transported across the inner mitochondrial membrane into the outer mitochondrial compartment. The H+ ions then flow back through special pores in the membrane, a process that is thought to drive the process of ATP synthesis. c) net yield of 34 ATP per glucose molecule d) 6 H2O are formed when the electrons unite with O2* at the end of electron transport chain. [* Note: This is the function of oxygen in living organisms!] Glycolysis occurs in the cytoplasm Kreb Cycle occurs in the mitochondria Electron Transport Chain occurs in the mitochondria Chemosismosis: electrons are released from NADH and from FADH2 and as they are passed along the series of enzymes, they give up energy which is used to fuel a process called chemiosmosis by which H+ ions are actively transported across the inner mitochondrial membrane into the outer mitochondrial compartment. Photophosphorylation: ATP a second product made during the light reaction Fermentation: an anaerobic respiration in which glucose is broken down to pyruvate during glycolysis. There is only a net gain of 2 ATP. There will be no Kreb Cycle or Electron Transport Chain Two types of Fermentation: › Lactic Acid Fermentation: The production of lactic acid without oxygen Examples: Milk products and muscles being oxygen deficient › Alcohol Fermentation: The production of ethyl alcohol and carbon dioxide Examples: Yeast (Bread and Alcoholic Beverages) Two parts to photosynthesis are: › Light (light dependent) reaction: Occurs in the thylakoid membrane(contains chlorophyll) Inputs to the light reactions are water and light Products: ATP, NADPH, and O2 Oxygen produced in the light reactions comes from H2O and not CO2 › Light Independent Reaction (dark reaction): Occurs in the stroma Inputs into the Calvin cycle are NADPH, ATP, and CO2 More ATP is used than NADPH creating a need for cylic photophosphorylation to create enough ATP for reaction The carbon of the sugar produced in photosynthesis comes from the CO2 of the Calvin Cycle Transpiration is the process of water evaporating out of the leaves. When the water goes out of the leaves the water the other parts of plants replace the water through the process known as the Cohesion Tension Theory Most photosynthesis takes place in the mesophyll portion of the leaf Mesophyll