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Bio.203-1-4.Intro
Molecular Biology Ch. 1 through 4 - Introduction to Biology
| Question | Answer |
|---|---|
| What is biology? | The scientific study of life |
| What is life defined by? | 1. Order, 2. Evolutionary adaptation, 3. Response to environment, 4. Reproduction, 5. Growth/development, 6. Energy processing, 7. Regulation |
| Emergent properties | Properties of life which are uncovered as you “zoom out” from lower levels. This occurs because of the arrangement and interactions of parts as complexity increases |
| Systems biology | An approach that attempts to model the dynamic behavior of whole biological systems based on a study of the interactions among the systems’ parts. |
| Systems of the earth, i.e., “levels of biological organization” | Biosphere, ecosystems (living and nonliving components of an area), communities (array of organisms in an ecosystem), populations (particular species), organisms, organs/organ systems, tissues, cells, organelles, molecules. |
| Eukaryotic cell | Subdivided by internal membranes into various membrane-enclosed organelles. In most eukaryotic cells the nucleus is the largest organelle. The other organelles are located in the cytoplasm (the non-nucleus portion) |
| Prokaryotic cell | Generally smaller and simpler than eukaryotic cells. The DNA is not separated from the rest of the cell via a nucleus. They also lack other kinds of organelles found in eukaryotic cells. |
| Nucleotides | Molecules that, when joined together, make up the structural units of RNA and DNA. E.g. Adenine, guanine, cytosine, thymine, and uracil |
| Gene expression | The entire process by which proteins are generated from DNA. DNA -> RNA -> proteins. |
| Are all RNA molecules translated into protein? | No, some RNAs carry out other important tasks. Some functions include regulating the functioning of protein-coding genes. |
| Genome | The entire “library” of genetic instructions that an organism inherits is called the genome |
| Genomics | Sequencing genes of multiple species and comparing them to one-another |
| What is sequencing? | Determining order of nucleotide bases |
| Bioinformatics | Using computational tools to store, organize, and analyze the huge volume of data that result from high-throughput methods |
| “High-throughput” refers to … | Quickly conducting millions of tests |
| Feedback regulation | The output of a process regulates the process |
| Negative feedback | Accumulation of the end product of a process slows down the process. |
| Example of negative feedback | The cell’s breakdown of sugar generated chemical energy in the form of ATP. When the cell makes more ATP than it can use, the excess ATP inhibits an enzyme at the beginning of the process |
| Positive feedback | The end-product speeds up its own production |
| Example of positive feedback | Blood clotting: chemicals released by clotting platelets attract more platelets. |
| Energy | Capacity to cause change, for instance by doing work |
| Potential energy | The energy matter possesses because of its position or structure |
| The fundamental characteristic of living organisms is | Their use of energy to carry out life’s activities. Living organisms transform energy from one form to another. |
| 3 domains of life | Domain bacteria (prokaryote), domain Archaea (prokaryote), and domain Eukarya (eukaryote) |
| Domain bacteria – how prevalent are they? | Most diverse and widespread prokaryotes |
| Domain Archaea | Most live in earth’s extreme environments, such as salty lakes and hot springs |
| Domain Eukarya, kingdoms | 1. Kingdom plantae, 2. Kingdom fungi, 3. Kingdom animalia, 4. protists (unicellular eukaryotes) |
| Unity underlying the diversity of life | There are a tremendous number of similarities between organisms. E.g. the architecture of the cilia in a paramecium is exactly the same as that of the cilia in our trachea. |
| Essential elements | Elements organisms need to live a healthy life and reproduce. Humans need 25 elements, plants need only 17 |
| What 6 elements make up 97% of living organisms? | H, N, O, C, P, S |
| Trace elements | An element required by life but found in minute quantities. E.g. iodine (processed by the thyroid) |
| Why do opiates relieve pain and alter mood? | They have similar chemical shapes to endorphins and bind to endorphin receptors in the brain |
| What percentage of the earth’s surface is water? | 75% |
| Four emergent properties of water that contribute to the earth’s suitability for life | 1. Cohesion of water molecules, 2. Moderation of temperature by water, 3. Floating ice on liquid water, 4. Solvency |
| How does the high specific heat of water affect climate? | By absorbing or releasing heat, oceans moderate coastal climates. In SoCal, the water absorbs a lot of heat; otherwise San Diego would be very hot like Palm Springs. |
| Evaporation | Molecules moving fast enough to escape attractions to each other and transform into a gas. Even at low temperatures, molecules occasionally escape, which is why water still evaporates in normal temperature. |
| Heat of vaporization | Quantity of heat a liquid must absorb for 1g of it to be converted from liquid to gas. Because of hydrogen bonds, water has a high heat of vaporization. |
| Evaporative cooling | Occurs because the hottest molecules are most likely to leave the gas because they’re moving fastest |
| Cohesion of water molecules | Occurs as a result of hydrogen bonding. Water sticks to each other which is why droplets of water form a spherical shape and also leads to high surface tension |
| Adhesion of water | Describes water clinging to other things, e.g. walls. |
| Moderation of temperature by water | Water absorbs heat from air that is warmer and releases stored heat to air that is cooler. Water is effective as a heat bank because it can absorb/release large amounts of heat with only a slight change to its own temperature. |
| Kinetic energy | Energy of motion, measured by heat |
| Temperature | Measure of heat intensity that represents average kinetic energy of molecules |
| Calorie & kilocal | Calorie: amount of heat it takes to raise the temperature of 1g of water by 1deg Celsius. Equal to 4.84J. Kilocal: 1,000 calories, equivalent to 1 food Calorie |
| Water’s specific heat | The ability of water to stabilize temperature stems from its relatively high specific heat. That is, the amount of heat that must be absorbed or lost for 1g of that substance to change its temp by 1deg Celsius. Water: 1cal/g |
| Hydration shell | Sphere of water molecules surrounding dissolved ions, separating and shielding them from one another. |
| Hydrophilic | Substance that has an affinity for water |
| Colloid | A stable suspension of fine particles, e.g. hydrophilic proteins too large to be dissolved |
| Why does water have a high specific heat? | Because of hydrogen bonding. So much heat is dedicated to breaking the hydrogen bonds before the molecules can actually start moving faster. |
| How the human blood buffers pH | One way is via carbonic acid (H2CO3), which is formed when CO2 reacts with water in blood plasma. If H+ begins to fall, carbonic acid dissociates and replenishes H+. If it rises, it reacts with HCO3- to form carbonic acid. |
| Acid precipitation | Rain, snow, or fog with a pH lower than 5.2. This can happen as a side effect of ocean acidification. |
| Amphipathic molecules | They contain both hydrophilic and hydrophobic parts |
| Max number of hydrogen bonds a water molecule can form | 4 |
| Why is carbon important? | Its versatility allows it to form molecules that are large, complex, and varied, making possible the diversity of organisms that have evolved |
| Vitalism | Vitalism was the belief in a life force outside jurisdiction of physical and chemical laws. It crumbled when it was proven that organic compounds could be synthesized artificially |
| Stanly Miller Experiment | Miller concluded that complex organic molecules could arise spontaneously under conditions thought to have existed on early Earth, mimicking volcanic eruptions. |
| Carbon’s electron configuration; why is this important? | 4 valence electrons on its second shell. It can branch off in 4 directions making it very versatile |
| Side note: chemical formula of urea | CO(NH2) |
| Hydrocarbons | Consisting of only carbon and hydrogen. E.g. methane, ethane, propane, butane |
| Why are hydrocarbons called fossil fuels | Because they’re comprised of organic materials left over from decomposed remains of organism that lived millions of years ago |
| Hydrocarbons in fats | Adipose tissue contains long hydrocarbon tails. This is because mammals need to store them as fuel reserve (they can be broken down to provide energy) |
| Organic chemistry | Branch of chemistry that specializes in the study of carbon compounds |
| Isomers | Variation in the architecture of organic molecules. Compounds that have the same numbers of atoms/same elements, but different structures |
| 3 types of isomers | Structural isomers, cis-trans isomers, and enantiomers |
| Structural isomers | Differ in the covalent arrangement of their atoms |
| Cis-trans isomers | Same covalent arrangement, but different special arrangement. Cis = on same side, trans = on opposing sides |
| Enantiomers | Differ in spatial arrangement around an asymmetric (or "chiral") carbon, resulting in mirror images, life Left and Right hands. L = levo, R = dextro. |
| Asymmetric carbon | One that is attached to four DIFFERENT atoms or groups. |
| Functional groups | Groups of atoms attached to the carbon skeletons of organic molecules and involved in chemical reactions. E.g. testosterone and estrogen have the same carbon skeleton but different functional groups. |
| Seven functional groups most important in biological processes | Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl. All of them except methyl are hydrophilic and thus increase solubility of organic compounds in water. Methyl is not reactive. |
| Amino group: name of compounds, example, properties | NH2: Amines. Glycine is a compound that has both amine and carboxyl groups. Such a compound is called an amino acid. Acts as a base, can pick up H+ from the surrounding solution (water, in living organisms) |
| Carboxyl group: name of compounds, example, properties | COOH: Carboxylic acids, or organic acids. Acetic acid, which gives vinegar its sour taste. Acts as an acid; it can donate H+ because the covalent bond between oxygen and hydrogen is so poal |
| Hydroxyl group: name of compounds, example, properties | OH: Alcohols. Ethanol (in alcoholic beverages). It is polar and can form hydrogen bonds with water, helping dissolve organic compounds such as sugars. |
| Carbonyl group: name of compounds, example, properties | CO: ketones (if carbonyl group is within the carbon skeleton) or aldehydes (if group is at the end of the carbon skeleton). Acetone (the simplest ketone). Found in sugars, giving rise to major types: ketoses/aldoses. |
| Sulfhydryl group: name of compounds, example, properties | SH: thiols. Cysteine, an important sulfur-containing amino acid. Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Also, the cross-linking can make hair curly. |
| Phosphate group: name of compounds, example, properties | OPO3^2-. Organic phosphates. Glyceral phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes. It contributes a negative charge to the molecule of which its part. |
| Methyl group: name of compounds, example, properties | CH3: methylated compounds. 5-methyl cytidine, a component of DNA that has been modified by an addition of a methyl group. Addition of a methyl group to DNA affects the expression of genes. |
| Adenosine triphosphate | ATP. Organic molecule called adenosine attached to a string of 3 phosphate groups. When ATP reacts with water, a phosphate group falls off (ATP becomes ADP). This reaction releases energy which can be used by a cell. |
| Solvation | Water molecules surrounding ions and neutralizing their charges. |
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