Biology Exam Notes 25 M/C 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20.

21. 22. 23. 24. 25.

periodic table;mass number, etc. isomers H-H bonding different bonds in the macro molecules amino acid types or reactions; condensation, dehydration, etc. difference between exothermic/endothermic and endergonic/exergonic ch.2&3 cofactors/coenzyme redox reaction anaerobic respiration/ch. 2 alternative pathways alt. pathway ethanol photosynthesis photosynthesis dna replication genetic code lac operon mRNA a chromotin fiber/ width operon blunt/sticky ends endosymbiotic steriod/hormone exert their effect by... homeostasis homeostasis

5 out of 8 Short Answers 1. characteristics of H2O 2. dna experiments; must be able to draw and explain 3. know RNA/DNA protein and what role do they have 4. 4 parts: respiration;stages, reactants, products, netp atp 5. photosynthesis/why the leaves change colour with season 6. ch.4&5 explain experiment 7. enyzmes in DNA replication 8. list all function groups and where M/C Element on periodic table:top number, mass number, number of protons and neutrons bottom number, atomic number, number of electrons isotopes- same atomic number but different mass number. difference is the number of neutrons pg. 22 electronegativity is the affinity of an atom to attract electrons in a covalent bond. 0 -> 1.7 (non-polar covalent) 1.7 ->4.2 (ionic) isomers - molecules with the same chemical formula but with a different arrangment of atoms; ex. alphaglucose, beta-glucose pg. 30 H-H bonding is the strongest intermolecular forces; strong dipole-dipole forces that form between an electropositive H of one polar molecule and an electronegative N, O, or F.

Water molecules are hold each onto each onto each other by H-H bonds and gives water the unique properties and angular shapes. pg. 17 Macromolecule bonds/functional bonds pg. 25, 28, 54 Carbohydrates / simple sugars (glucose) Lipid / glycerol and fatty acids protein / amino acids nucleic acid / nucleotides Carbohydrates/glycosidic linkage - covalent bonds holding monosaccharides to each other that are formed by condensation (removal of water) which the H atom from hydroxyl group of one sugar and the -OH group comes from a hydroxyl group of the other pg. 30 Lipids/ester linkage - a functional group linkage formed by condensation of a carboxyl group and a hydroxyl group;between the glycerol and the fatty acid. pg. 37 Proteins/peptide bond - the amide linkage that holds amino acids together in polypeptides; occurs by condensation between the oxygen from the carboxyl group and the H atoms from the amino group of an adjacent amino acid. pg. 41, 43 Nucleic acid/phosphodiester linkage - links between nucleotides by a phosphate group There are 20 different amino acids and are the side chains in an amino acid. there is a terminal amino group and a terminal carboxyl group on each end of a polypeptide ( more than one amino acid). pg. 41-43 Condensation(Dehydration) Rx - creates a covalent bond between 2 subunits; removes a water molecule, by a removal of an H atom and an -OH group from the other subunits functinal group. Anabolic Rx - reaction that produces a large molecule from smaller subunits Hydrolysis Rx - a water molecule is used to break a covalent bond from a large molecule to smaller subunits Catabolic Rx - reactions that break macromolecules into individual subunits;; pg. 28 Endergonic/Endothermic Rx - a chemical Rx in which the energy of the products is more than the energy of the reactants. Exergonic/Exothermic Rx - a chemical Rx in which the energy of the products is less than the energy of the reactants; bonds become more stable. pg. 60, 64 Cofactors - nonprotein components, such as dissolved ions, that are needed for some enzymes to function Coenzymes - organic nonprotein cofactors that are needed for some enzymes to function pg. 72 NAD+, NADP+, FAD+:transport of protons (H+) and electrons from one reaction site to another NAD+ to NADH - coenzyme used to shuttles electrons to the first component of the electron transport chain into the mitochondrial inner membrane. also used in photosynthesis ( pg. 147) FAD to FADH2- is similar to NAD+ as they are energy-harvesting reactions that will eventually transfer most of their free energy to ATP molecules. the reduced coenzymes act as mobile energy carriers within the cell. pg. 95-96. coenzyme A attaches to remaining acetic acid to produce acetyl-CoA which will be used in the Kreb Cycle. pg. 94, 101 Calvin cycle is relevant as it recycles the coenzyme of rubisco that catalyzes the first reaction and the oxidation of RuBP to phospho-glycolate. pg. 162 Redox Rx - a chemical Rx involving the transfer of one or more electrons from one atom to another; a reaction in which oxidation and reduction occur. Pg. 66-67 Oxidation - atom loses one or more electrons Reduction - atom gains one or more electrons Oxidizing agent - the substance that gains an electron Reducing agent - the substance that loses an electron A coupled redox reaction, is when the product of one reaction is the reactant of the next series.

reduced>oxidized>reduced, etc. The electron moves to successively stronger electron acceptors, free energy is released in each step. ***remember the question on the test that asks about the stronger bonds,whether it was the one previously reduced/oxidized. Anaerobic respiration is the cellular respiration without oxygen as the final electron acceptor. Glycolysis allows organisms to obtain energy from nutrients in the absence of oxygen, but in step 6 (G3P to BPB) of the glycolytic pathways reduced NAD+ to NADH+ and cells possess a limited supply of NAD+. Thus if cells continue w/o a mechanism to oxidize NADH back to NAD+, step 6 will be blocked and glycolysis will discontinue. In aerobic respiration the ETC oxidizes NADH back to NAD+. Therefore, fermentation is the alternate to process without oxygen and the ETC through various bacterias. Ethanol fermentation - NADH passes its hydrogen atoms to acetaldehyde (when CO2 is removed from pyruvate). This forms ethanol and allows NAD+ to be recycled and glycolysis to continue. Pg. 119 Lactate (Lactic Acid) Fermentation - NADH produced transfers its hydrogen atoms to pyruvate in the cytoplasm of the cell, regenerating NAD+ and allows glycolysis to continue. Pg. 120 Photosynthesis can be broken down to three stages: Stage 1: Light Reactions Stage 2: Synthesize ATP and NADPH Stage 3: Calvin Cycle Chlorophyll A is the only pigment that can transfer the light energy to the carbon fixation reactions in photosynthesis. Chlorophyll b and carotene are accessory pigments that transfer their energy to chlor.A. The main objective of the Calvin cycle is to produce G3P. It takes 6 turns of the cycle to produce one 6-carbon glucose molecule. 3 CO2 = 1 3-G3P molecule. Light reactions occur on the thylakoid membranes in the chloroplast. Calvin cycle occurs in the stroma. C4 plants reduce photorespiration by continuously pumping CO2 by a two part compartment of a mesophyll cell and bundle-sheath cell. CAM plants closes stomata during the day to reserve water and opens at night incorporating the CO2 accumulated in the air. ***review chart on pg. 181 DNA replication occurs semiconservatively, where each replication is composed of one parent strand and one synthesized strand. ****review process of DNA replication. pg. 219 review genetic code pg. 240 Lac operon - a cluster of genes under the control of one promoter and one operator; the genes collectively code for the enzymes and proteins required for a bacterial cell to use lactose as a nutrient Lacl protein - a repressor protein that binds to the lac operon operator, preventing RNA polymerase from transcribing the lac operon genes. Therefore, if there is no lactose present, the genes are not transcribed. When there is lactose present, it binds to the protein causing it to fall off the operator and allowing the genes to be transcribed. Lactose is the signal molecule/inducer. TRP operon is similar to lac operon, but if there are high levels of tryptophan, then the operon is repressed. the product which is tryptophan, is the corepressor as it binds to trp repressor protein which then binds to the operator.

mRNA - the end product of transcription of a gene, mRNA is translated by ribosomes into protein. The synthesis of mRNA can be put into three stages: initiation, elongation, termination. Initiation - RNA polymerase binds upstream at promoter region, then DNA is unwound, exposing the

template strand. Elongation - synthesized 5-3. Uracil - Adenine. Termination - mRNA and RNA polymerase are released. 5 cap is added to the start, signaling as the beginning of translation. poly-A tail is added, a string of 200 to 300 adenine base pairs to protect from degradation. Introns are cut by spliceosomes then exons are joined together. chromatin fiber diameter is about 30nm-40nm sticky end - fragment end of a DNA molecule with short single- stranded overhangs, resulting from cleavage by a restriction enzyme blunt end - fragment ends of a DNA molecule that are fully base paired, resulting from cleavage by a restriction enzyme

The endosymbiotic theory proposes that an ancestor of cyanobacteria was engulfed by an ancestor of todays eukaryotic cell and gave rise to plant cells.
endosymbiotic - physical and chemical contact between one species and another species living within its body, which is beneficial to at least one of the species. pg. 265 steroid hormones exert their efforts by entering the nucleus of a cell and initiating or altering the

expression of a gene.
homeostasis - process by which a constant internal environment is maintained despite changes in the external environment Review homeostasis pg. 332

Characteristics of Water - pg. 19 1. colourless, odourless, tasteless and can be solid, liquid or a gas. 2. Its polar covalent bonds and asymmetrical structure makes it a highly polar molecule. 3. Water is very soluble because it provides partial positive and negative charges. 4. WATER CLINGS Cohesive - form hydrogen bonds with each other = high surface tension Adhesive - form hydrogen bonds with polar materials = capillary action 5. WATER ABSORBS LOTS OF HEAT High specific heat capacity - hydrogen bonding causes water to absorb a large amount of heat before its temperature increases and lose large amounts of heat before its temperature decreases = temperature modification ( helps organisms maintain body temp/homeostasis). High specific heat vaporization - H. bonding causes liquid water to absorb a large amount of heat to become a vapour = evaporative cooling (like sweating to dissipate heat) 6. SOLID WATER IS LESS DENSE THAN LIQUID WATER Highest density @ 4 degrees C - under 0 degrees, the V-shaped molecules reduces the the density (ice floats on water). 7. Hydrogen bonding accounts for the following properties of water: high solubility of polar and

ionic substances, cohesion, adhesion, high surface tension, capillarity, high specific heat capacity, and high specific heat of vaporization.
DNA experiments Hammerling: to find the location of the hereditary information pg. 206-207 used an alga that contained a cap, stock and a foot where the nucleus is located. Experiment 1: removed the cap, and the cap regenerated. Experiment 2: removed the foot, and did not regenerated.

concluded that the DNA is located in the nucleus.

Hershey/Chase: to confirm that DNA is the hereditary information. pg. 208-209 They used a virus that would infect a bacterial host. Protein coat was tagged with an isotope of sulfur (35S) while the DNA with an isotope of phosphorus (32P). Found that the bacteria that were exposed to the tagged protein coats, did not contain the 35S but was in the medium. The bacteria that was exposed to the tagged DNA, 32P was found in the cell. The results of Hershey and Chases experiments showed that only the DNA from the

bacteriophage, and not the protein coat, enters the bacteria to direct the synthesis of new viral DNA and new viral protein coats. Meselson/Stahl: to suggest that DNA was replicated semiconservatively. pg. 217-218
They grew a bacteria in a medium rich in a heavy nitrogen isotope 15N and was grown for 17 generations.

All the DNA after one generation after the switch to 14N would consist of one 14N strand and one 15N strand. The isolated DNA should settle as one band of intermediate density after centrifugation. After two generations, half of the DNA would have a density like that after one generation, while the other half would have a density similar to the 14N DNA. Therefore, two different bands would be present in the gradient, one of intermediate and one of light density.
semiconservative - process of replication in which each DNA molecule is composed of one parent strand and one newly synthesized strand.

Roles of RNA/DNA/Protein DNA pg. 210 - a double-stranded polymer of nucleotides (each consisting of a deoxyribose sugar, a phosphate, and four nitrogenous bases) that carries the genetic information of an organism Purines: Adenine + Guanine ; Pyrimidines: Thymine + Cytosine nitrogenous base attached at 1 and phosphate at 5 of the sugar ; form phosphodiester bonds. Is the template strand for the mRNA. RNA pg.237 - uracil instead of thymine and binds to adenine. also, uses a ribose sugar, which has a hydroxyl (-OH) group on the 2 carbon. it is also single stranded and able to leave the nucleus. mRNA pg.238, 242 - the end product of transcription of a gene, mRNA is translated by ribosomes into protein. It is the intermediate between and the ribosome, is the carrier of the information from the DNA. tRNA pg. 238, 250-251- a form of RNA that is responsible for delivering amino acids to the ribosomes during the process of translation and synthesize proteins. At one arm of the tRNA, the anticodon recognizes the codon of the mRNA and the opposite arm carries the corresponding amino acid. if the mRNA has UAU, the anticodon on the tRNA has AUA. one tRNA only has one amino acid. aminoacyltRNA - A tRNA molecule with its corresponding amino acid attached to its acceptor site at the 3 end. The enzymes responsible for adding the appropriate amino acid to each tRNA is called a-tRNA synthetase. rRNA pg. 250- a form of RNA that binds with ribosomal protein to form ribosomes Ribosomes consist of a large subunit and a small subunit. The subunits are a combination of ribosomal RNA (rRNA) and protein. Photosynthesis: Why do the leaves change colours with the season pg. 152-154 Summer leaves contain chlorophyll and accessory pigments, but the green colour of chlorophyll overwhelms the colours reflected by the accessory pigments. Autumn leaves contain less chlorophyll, causing the colours of the accessory and other pigments to become visible. In spring and summer, leaves appear green because of the high concentration of chlorophyll.

Xanthophyll (yellow), carotenoids (yellow-orange), and anthocyanins (red, violet, and blue) are

overwhelmed by the green light reflected by chlorophyll. In autumn, plants stop producing chlorophyll, causing the yellow, red, and brown colours of autumn leaves to show. Another chemical in leaves, auxin, controls a special band of cells at the base of each leaf stem, called the abscission layer. During the growing season, auxin prevents this layer from fully developing and blocking the tiny, internal tubes that connect each leaf to the rest of the trees circulatory system. In fall, however, cooler and shorter days trigger an end to auxin production, allowing the abscission layer to grow and cut off the circulation of water, nutrients and sugar to the leaves.

Enzymes involved in DNA Replication DNA polymerase III - the enzyme responsible for synthesizing complementary strands of DNA during DNA
replication DNA helicase - the enzyme that unwinds double-helical DNA by disrupting hydrogen bonds single-stranded binding proteins (SSBs) - a protein that keeps separated strands of DNA apart DNA gyrase - the bacterial enzyme that relieves the tension produced by the unwinding of DNA during replication RNA (ribonucleic acid) primer - a sequence of 10 to 60 RNA bases that is annealed to a region of singlestranded DNA for the purpose of initiating DNA replication primase - the enzyme that builds RNA primers DNA polymerase I - an enzyme that removes RNA primers and replaces them with the appropriate deoxyribonucleotides during DNA replication DNA ligase - the enzyme that joins DNA fragments together by catalyzing the formation of a bond between the 3 hydroxyl group and a 5 phosphate group on the sugar phosphate backbones exonuclease - an enzyme that cuts out nucleotides at the end of a DNA strand