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Biology Test #1
Biology 1009 Flashcards for Exam #1
| Question | Answer |
|---|---|
| What are the major elements found in living organisms? | Hydrogen, Oxygen, Carbon, and Nitrogen. |
| What are the minor elements found in living organisms? | Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, and Magnesium. |
| What are common trace elements? | Zinc, Copper, Cobalt, Manganese, and Iron. |
| What are isotopes? | Elements that have the same properties (same number of protons and electrons), but different masses (different number of neutrons). |
| Why are water molecules polar? | Unequal sharing of the bonding electrons. (Note: The O end of the molecule is slightly negatively charged and the H end are slightly positively charged). |
| How is bond strength determined? | Measured in the amount of energy required to break the bond. |
| What is the order of bond strength (starting with the strongest)? | Colvalent bonds (200-400 kJ/mole), Ionic bonds (40-85 kJ/mole), and H bonds (17-20 kJ/mole). |
| What is unique about water? | -Has high freezing and boiling points. -Solid is less dense than liquid. -Has a high surface tension. -Acts as a temperature buffer (has a high heat capacity). -Is a good solvent. -Can ionize. |
| What is pH? | pH= -log [H+] |
| What pH levels are: neutral, acidic, and basic? | -pH of 7 is neutral. -pH of less than 7 is acidic. -pH of greater than 7 is basic. |
| What are buffers? | Compounds that help to maintain constant pH when acid or base is added to a system by binding the excess H+ ions. |
| What are hydrocarbons? | Molecules that only consist of H and O. |
| What is a hydroxyl group? | C—O ... Compounds with OH groups can be organic alcohols, e.g., ethanol CH3—CH2—OH |
| What is an aldehyde? | H—C=O ... When this group appears at the end of a carbon chain. |
| What is a ketone? | When the C=O is found in the middle of a carbon chain. |
| What is a organic acid? (Also known as carboxly group) | When OH is bonded to C=O at the end of a hydrocarbon chain. It can lose an H+ in solution and is often shown in its ionized form. |
| What are other groups often found in biological molecules? | Phosphate groups (O-PO3 2-) , amino groups (NH2), and sulfhydryl groups (SH). |
| What are the 4 major groups of carbon compounds that are important in all living organisms? | Carbohydrates Lipids (Fats) Amino acids and Proteins Nucleotides and Nucleic Acid |
| What are carbohydrates? | Polymers of sugar. |
| What are sugars? | Polyhydroxy aldehydes or ketones. |
| What is the common formula for sugars? | (CH2O)n with n = 5 or 6 occurring most often. Glucose and fructose are both 6 carbon sugars with the molecular formula, C6H12O6. |
| What happens to sugars when they are in a solution? | Will form ring structures. |
| How can complex carbohydrates be formed? | By removing water and connecting the sugars by a C---O---C bond (glycosidic bond). |
| What are a couple examples of complex carbohydrates? | Starch and cellulose. |
| What is starch? | Starch is a polymer of alpha-glucose which is produced by plants. It is a major component of the human diet. Humans have enzymes that can break the alpha-1,4 linkage and provide free glucose for cellular metabolism. |
| What is cellulose? | Polymer of beta-glucose and is found in plant cell walls. Humans and most animals cannot break the beta-1,4 linkage to free the glucose units. Herbivores, such as cows, have bacteria in their rumen that can digest cellulose. |
| What are lipids (fats)? | Macromolecules composed of glycerol and fatty acids. Fatty acids are long chains of carbons with an organic acid group at one end. |
| What makes a fatty acid saturated? | No double bonds in the C chain. (Note: Saturated fats have higher melting temperatures than unsaturated fats). |
| What makes a fatty acid unsaturated? | One or more double bonds. The double bonds found in unsaturated fatty acids are rigid compared to C-C single bonds. |
| What makes a cis- unsaturated fatty acid? | The H's are arranged around the double bond on the same side. Cis fatty acids are the most common isomers in living organisms. |
| What makes a trans- unsaturated fatty acid? | The H's are arranged around the double bond across from each other. Trans fatty acids are unusual and too much in your diet can lead to heart disease. |
| How do fatty acids attach to glycerol? | By removing water. The fatty acids are attached by an ester bond. The resulting compound is called a triglyceride and is a storage form of carbon. |
| What are phospholipids? | Some lipids have two fatty acids attached to glycerol and a phosphate group with an additional constituent attached in the third position. |
| What are proteins? | Polymers of amino acids formed by removing water and making a peptide bond. There are 20 different amino acids commonly found in proteins. |
| What do all amino acids except glycine have? | A chiral center ( i.e., a carbon that is bonded to four different chemical groups). There are two ways to arrange the groups around the chiral center in 3dimensional space which produces mirror images. Most "L handed" isomer. |
| What is the primary level of structure of proteins? | Sequence of amino acids connected by peptide bond. |
| What is the secondary level of structure of proteins? | Amino acids that are near each other form alpha helices or beta strands that are held together by H bonds. |
| What is the tertiary level of structure of proteins? | Global folding of the molecule in 3 dimensions. Stabilized by: hydrophobic ―bonds, H bonds, Ionic bonds and Disulfide bonds. Except for the disulfide bridge, most of the bonds that maintain the tertiary structure are weak bonds and easily broken. |
| What is the quaternary level of structure of proteins? | Associations of proteins with other proteins such as the alpha and beta subunits of the protein, hemoglobin. Quaternary structures are stabilized by hydrophobic, H, and ionic bonds. |
| What are nucleic acids? | Polymers of nucleotides. |
| What are the three components of nucleotides? | 1. sugar - usually a 5 C, ribose or deoxyribose 2. a nitrogenous base --- purines and pyrimidines 3. a phosphate group |
| What is ATP? | Adenosine tri-phosphate. Is a nucleotide involved in energy–requiring reactions. |
| How do you polymerize nucleotides? | By removing water to form phosphate ester bonds between the sugars. These can form large, complex nucleic acids such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). |
| How is the limit of the resolution of the light microscope determined? | By the wavelength of visible light. |
| How does the electron microscope work? | Uses magnetic lenses and an electron beam for illumination. The transmission EM shows internal structures of cells; the scanning EM shows surface details. |
| What are prokaroyotes? Give examples. | Single-celled organisms with very little internal membranous organization. Prokaryotes include bacteria and archaea. |
| What are the common shapes of prokaroyotes? | Spheres (cocci), rods (bacilli), or spiral. Typical size is 1-10 micro meters. |
| What is the cell wall of composed of? | Protein and carbohydrate. |
| What is the cell membrane? | Proteins in a lipid bi-layer. |
| What is ribosomes? | Granular material in the cytoplasm composed of RNA and protein. Ribosomes are the sites of new protein synthesis. |
| What are viruses? | Consist of a protein coat with nucleic acid (RNA or DNA) on the inside. Some viruses also have carbohydrates on their exterior. Viruses can reproduce only inside other living cells. |
| What is the endoplasmic reticulum(ER)? | A system of membranes that runs through the cytoplasm; it transports molecules to various locations in the cell. -Rough ER - has ribosomes attached; proteins enter the ER after synthesis. -Smooth ER - membranes have no attached ribosomes. |
| What is the golgi apparatus? | A membrane “stack” that processes proteins, packages them for transport in Golgi vesicles. |
| What is the mitochondria? | Organelles with a double membrane that function in oxidative metabolism and energy production. The inner membrane has extensive fingerlike projections. The soluble portion inside the mitochondrion is called the matrix. |
| What are chloroplasts? | Organelles with three membranes, an outer and inner membrane and internal membranes called thylakoids. The soluble portion inside this organelle is called the stroma. The chloroplast is the site of photosynthesis in plants and eukaryotic algae. |
| What is the cytoskeleton? | Long strands running through the cytoplasm made of microtubules and microfilaments. Microtubules are made of a protein called tubulin. Microfilaments are composed of a protein called actin. |
| What is a lysosome? | An organelle with a single membrane. Digestive proteins inside break down defective macromolecules, organelles, and ingested material. |
| What are the features of membranes? | 1. Are 6-10 nm thick. 2. Are composed of lipid and protein (the membrane is about 50:50). 3. The basic structure is a lipid bilayer formed from phospholipids. 4. Contain proteins that are characteristic of the type of membrane. 5. Are asymmetric. |
| What is diffusion? | The movement of molecules from higher to lower concentration. The rate of diffusion will depend on molecular size and environmental parameters such as temperature and viscosity. |
| What can readily penetrate cell membranes? | Hydrophobic molecules, especially small ones. (e.g., oxygen, benzene) |
| What molecules can diffuse through the lipid bilayer? | Small polar molecules (e.g. glycerol, ethanol). |
| What is osmosis? | The diffusion of water through a semi-permeable membrane. |
| What does the lipid bilayer not impede the flow of water? | Water is a small molecule and the most common compound in living systems. Lipids in the bilayer are not covalently bonded to each other; so temporary “holes” in the bilayer allow water to flow through it. Water flows from higher to lower concentration. |
| What is a hypotonic solution? | More water in solution (less solute) than in the cell; water flows in and the cell swells. Cells with walls can tolerate a hypotonic environment. |
| What is an isotonic solution? | The same amount of water inside and outside the cell; no net movement of water. A solution of 0.15 M NaCl is isotonic for most animal cells. |
| What is a hypertonic solution? | Less water in solution (more solute) than in the cell; water flow out and the cell shrinks. |
| What does not freely pass through membranes? | Ions, polar molecules, and large molecules. (Integral membrane proteins make it possible for these to cross the bilayer). |
| What is facilitated diffusion? | Movement of molecules across the membrane from higher to lower concentration with the help of a carrier protein. No energy is required; example, the glucose-Na+ symporter. |
| What is active transport? | Movement of molecules across the membrane against the concentration gradient. In addition to an integral membrane protein, energy is required. This is usually the chemical bond energy in ATP. |
| What is exocytosis? | Vesicles expel substances out of the cell; e.g., Golgi vesicle. |
| What is Endocytosis (Pinocytosis)? | Uptake of molecules from the environment by vesicle formation. An example: uptake of Low Density Lipoproteins (LDL) containing cholesterol by cells. |
| What is phagocytosis? | Cell eating; uptake of large particles, bacteria, etc., by vesicle formation. Example: amoeba engulfing bacteria. |
| What is energy? | The capacity to do work. |
| What is the first law of thermodynamics? | Energy cannot be created or destroyed; the energy in any system is constant.` |
| What is the second law of thermodynamics? | The useful energy in any system is less than the total energy. ( delta(change in) G = delta E - T delta S. ) |
| What does "G" stand for? | Gibbs’ free energy; the energy that can be used to do work. |
| What does "E" stand for? | The total energy of the system (sometimes described as enthalpy, H). |
| What does "T" stand for? | Temperature in degree absolute (degrees Kelvin – degrees C + 273. |
| What does "S" stand for? | Entropy; non-usable forms of energy, disorder. |
| What does it mean if delta G is negative? | The reaction is exergonic; energy will be given off. The reaction is said to be “spontaneous”. |
| What does it mean if delta G is positive? | The reaction is endergonic; energy is required. The reaction will not proceed without the addition of external energy. |
| What does it mean if delta G is zero? | The reaction is at equilibrium. |
| How is activation energy provided? | It can be provided from the environment, such as heat or by a catalyst. |
| How do catalysts work? | Provide an alternative pathway and speed up chemical reactions. Only a small amount of catalysts is needed (it can turnover). |
| How do enzymes work? | Highly specific for a particular reaction because of their tertiary structure. The reactants (substrates) bind to an active site on the enzyme. After binding, there is the formation of a transient Enzyme-Substrate complex and product is produced. |
| When do enzymes work best? | When they are in at their optimum pH and temperature. Some enzymes require additional components called cofactors to be active. |
| What inhibits enzymes? | Agents that disrupt their tertiary structure such as heat, acid,heavy metals, and some chemicals such as ethanol. Enzymes that lose their tertiary structure are said to be “denatured”. |
| What are Redox reactions? | Oxidation-reduction reactions. Very common in cell metabolism and often have large ∆G values. |
| What is oxidation? | The loss of electrons. |
| What is reduction? | The gain of electrons. |
| What is an oxidizing agent? | A compound that will accept electrons during the course of a reaction. |
| What is a reducing agent? | A compound that will donate electrons during the course of a reaction. |
| What commonly accompanies electrons that are transferred in biological reactions? | H+ |
| What is the oxidation of glucose? | Glucose is oxidized slowly in several steps and the energy released is used to drive the synthesis of ATP. |
| What is glycolosis? | A series of 10 enzymatic reactions that occur in the cell cytoplasm. |
| What is the first (summarized) point in glycolosis? | 1. 1 glucose (C6H12O6) is broken down to 2 pyruvic acid molecules (C3H4O2). |
| What is the second (summarized) point in glycolosis? | 2. 4 ADP + Pi are used to produce 4 ATP/glucose. |
| What is the third (summarized) point in glycolosis? | 3. INPUT - 2 ATP is needed to activate glucose. |
| What is the fourth (summarized) point in glycolosis? | 4. NET GAIN - 2 ATP/glucose Approximately 3% efficiency. |
| What is the fifth (summarized) point in glycolosis? | 5. 2 NAD are reduced to 2 NADH. |
| What is the sixth (summarized) point in glycolosis? | No oxygen is required in glycolysis; this is anaerobic (without air) metabolism. |
| What is fermentation? | A process that allows organisms to live using only glycolysis to metabolize glucose. A mechanism to re-oxidize NADH is required to continue the redox step of glycolysis shown above (oxidation of glyceraldehyde-3-P). |
| What is one way fermentation occurs? | Pyruvic acid can be reduced to lactic acid; NADH is the reducing agent. pyruvic acid + NADH → lactic acid + NAD. (Organisms such as Lactobacillus spp. and animal muscle cells can do this reaction). |
| What is another way fermentation occurs? | Pyruvic acid can be decarboxylated to acetaldehyde and the aldehyde is then reduced to ethanol. pyruvic acid → acetaldehyde + CO2 → ethanol + NAD (note second arrow is NADH) |
| What is the citric acid (Kreb's cycle)? | In eukaryotic cells, pyruvic acid is transported into the matrix of the mitochondrion where aerobic metabolism takes place. In prokaryotes, this cycle occurs in the cytoplasm. No oxygen is used in this cycle. The reactions only yield a small amount of ATP |
| How does the citric acid cycle begin? | The condensation of acetyl-CoA and oxaloacetic acid to yield citric acid. |
| What is the rest of the citric acid cycle? | A series of 8 enzymatic reactions that results in the oxidation of the carbons in acetyl- CoA to CO2 and the regeneration of oxaloacetic acid. |
| How is most of the energy obtained by pyruvate used? | It is used to reduce the cofactors. |
| What is the electron transport system? | Consists of a series of integral membrane proteins and cofactors in the inner membrane (cristae) of the mitochondrion. (In bacteria, these proteins and cofactors are found in the cell membrane). |
| What is the function of the electron transport system? | To oxidize the cofactors and transfer the electrons to O2. NADH and FADH2 are oxidized to NAD and FAD; O2 is reduced to H2O. The proteins of the ETS also “pump” H+ ions into the inter-membrane space. |
| What is chemiosmotic coupling? | An ingenious method by which the cell uses membranes to couple the energy released by oxidation of the cofactors to produce ATP; the process is referred to as oxidative phosphorylation. |
| How much ATP does the complete oxidation of glucose yield? | Yields 30-36 moles of ATP per mole of glucose. Only about 35% of the chemical bond energy in glucose (-2800 kJ/mole) is retained as chemical bond energy in ATP. The rest of the energy is “lost” as heat. |
| What are endothermic organisms? | Organisms such as birds and mammals retain some of this heat and use it to keep a constant body temperature. This enables them to maintain a stable metabolic rate despite changes in the temperature of the environment. |
| What are ectothermic organisms? | Organisms such as amphibians, plants, and bacteria that do not retain the heat. Their metabolic rate is determined by the temperature of the environment. Q10 = 2; raising the temperature by 10 degrees C will double the metabolic rate. |
| Where are lipids generally metabolized? | In the mitochondrion. |
| How much energy do lipids yield? | About 4 times the energy of carbohydrates, 38 kJ/mole vs 17 kJ/mole. |
| Which takes up more space: lipids or carbohydrates? | Lipids are more easily stored in cells; they take up less space than carbohydrates. |
| Process of breaking down proteins. | Proteins are broken down to their constituent amino acids. Protein + H2O ---> amino acids protease or peptidase |
| What are amino acids used for? | Are not metabolized for energy under normal conditions, but are used to build new proteins. |
| How does metabolism start? | By the removal of the amino (NH2) group which can be recycled or excreted. The remainder of the carbon chain is usually metabolized by the Citric Acid Cycle. |
| How much does the metabolism of proteins yield? | Does not yield as much energy as metabolism of carbohydrates and lipids. |
| What drives photosynthesis? | The energy of visible light - 400-700 nm. |
| How much does green plant photosynthesis yield? | 6 CO2 + 6 H2O ⇒ C6H12O6 + 6 O2 ∆G = + 2800 kJ/mole. |
| How is the energy in wavelengths determined? | The energy in a particular wavelength is proportional to 1/λ, i.e., shorter wavelengths have higher energy. |
| What absorbs visible light? | Chlorophyll a. This pigment is present in all plants. The molecule consists of a large ring with a Mg2+ in the center and a long hydrocarbon chain. These properties make the molecule very hydrophobic. |
| What comprises chloroplasts? | Two outer membranes and a system of internal membranes called thylakoids. The thylakoids have a space inside called the thylakoid space or lumen. The soluble portion of the chloroplast is called the stroma. |
| Why does chlorophyll appear green? | It absorbs visible light in the blue and red regions of the spectrum and transmits green light. |
| What is photosynthesis? | A redox reaction where water is the reducing agent. |
| What is the first Redox reaction of photosynthesis? | Occurs in thylakoid membranes H2O is oxidized and O2 is released. NADP is reduced to NADPH ATP is synthesized. (ADP + Pi → ATP). |
| What is PSI? | A protein-pigment system integrated into the thylakoid membranes. Two reduced ferredoxins (a one electron carrier) reduce NADP to NADP. |
| What is Plastocyanin? | A peripheral membrane protein in the thylakoid lumen. It replaces the electron lost by PSI. Receives electrons from an Electron Transport System (ETS) in the thylakoid membrane. |
| What is PSII? | A protein-pigment system integrated into the thylakoid membranes. PSII also uses light energy to split H2O. |
| What is the second Redox reaction of photosynthesis? | CO2 Fixation. The reactions that produce fixed carbon are called the C-3 cycle. They are also referred to as the Calvin cycle after one of the lead researcher. The C-3 cycle does NOT occur in the dark. |
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