Week Two - Biology (Kinkle)

Explain the discrete energy levels in which electrons orbit the nucleus of an atom and how this is related to potential energy.

electrons and attracted to the positively charged nucleus (due to the fact that electrons are negatively charged.) the electrons have potential energy that is related to their position, and the amount of potential energy impacts how it orbits around the dense nucleus. to oppose the attraction of the nucleus and move the electron to a more distant orbital requires in input of energy, however. therefore, electrons have more potential energy. the energy levels within the atomic structure work to help with the orbital movement because every atom exhibits a ladder of potential energy values, a discrete set of orbitals at a particular energetic "distances" from the nucleus.

Define lipids, name the different types of lipids, and list the common uses of each in living organisms.

lipids definition: a non-polar hydrophobic organic molecule that is insoluble in water (which is polar) but dissolved readily in non polar organic solvents; includes fats, oils, waxes, steroids, phospholipids, and carotenoids. different types of lipids: 1) triglycerides - they are fat stored in the cells. when your body needs energy, triglycerides are used are released into your bloodstream to provide fuel for your muscles to work. 2) steroids - these are used as hormones in the body 3) phospholipids - they make up the membranes of our cells (phospholipid bilayer. the head is hydrophilic and the tail is hydrophobic. the heads point the outside (water) and the tails face the inside because it wants to avoid water.)

1) explain the nature of acids and bases, 2) and their relationship to the pH scale

1) pH is the concentration of hydrogen ions, and concurrently hydroxide ions, in a solution. 2) acids: any substance that dissociates in water to increase the H+ of a solution is called an acid. the stronger the acid is, the more hydrogen ions it produces and the lower its pH. bases: a substance that combines with H+ when dissolved in water, and this lowers the H+, is called a base. therefore, basic (also known as alkaline) solutions have a pH above 7.

Give two examples of how isotopes can be used in biological research and medicine

1) they can be used to carbon date fossils/ other materials by using their half-life information. by determining the ratios of the different isotopes of carbon and other elements in biological samples and in rocks, scientists are able to accurately determine when the fossils/ materials were made (up to thousands of years ago.) 2) radioactive isotopes can "tag" a specific molecule and then follow its progress in living cells/ tissue. (helpful for medical field)

Define compound

A substance consisting of two or more elements that are chemically combined.

Define element

A substance made of only one type of atom, and something that cannot be broken down into smaller parts.

Define atomic mass

The atomic mass is a weighted average of all of the isotopes of that element, in which the mass of each isotope is multiplied by the abundance of that particular isotope.

Define isotope

atoms with the same number of protons but different number of neutrons. "most elements in nature exist as mixtures of different isotopes. carbon, for example, has 3 isotopes, all containing 6 protons. over 99% of the carbon found in nature exists as an isotope that also contains 6 neutrons."

list common monosaccharides, their empirical formulas, and draw a picture of their overall structure. the exact arrangement of each -OH and -H group is not important for this class

common monosaccharides: 1) ribose (5 sugar carbon monosaccharide) 2) deoxyribose (5 sugar carbon monosaccharide) 3) glucose (6 carbon sugar monosaccharide) 4) fructose (6 carbon sugar monosaccharide) 5) galactose (6 carbon sugar monosaccharide) empirical formula for deoxyribose and ribose (5 carbon sugar monosaccharides, thus multiply CH2O by 5): C5H10O5 empirical formula for fructose, glucose and galactose (6 carbon sugar monosaccharide, thus multiply CH2O by 6): C6H12O6 general structures of each: *notice how the 5 carbon sugar monosaccharides (deoxyribose and ribose) are *pentagons*, and the 6 carbon sugar monosaccharides (glucose, fructose, and galactose) are *hexagons*.

draw the reactions that are involved in the formation of polymers from monomers, as well as the formation of monomers from polymers, naming each reaction and describing what is occurring.

draw the reactions: (picture shown) *polymers are made by dehydration, and they are broken down by hydrolysis.* the two reactions, as mentioned above, are hydrolysis and dehydration. dehydration is when the OH group from one monomer & H is removed from another monomer (AKA, H2O was taken away as shown in the photo), to form another covalent bond. hydrolysis is when a molecule of water is added, breaking the covalent bond.

describe the common variations found in fatty acids, and how they affect the chemistry and biology of triglycerides

*Fatty acids are long-chain hydrocarbons with a carboxyl group (COOH) at the end.* The variations found in fatty acids: 1) saturated 2) polyunsaturated 3) unsaturated. How these differences affect the chemistry and biology of triglycerides: 1) Saturated - if all of the internal carbon atoms in a fatty acid chain are bonded to two hydrogen atoms, it's called saturated (saturated refers to it having the maximum hydrogen atoms possible.) 2) Unsaturated - A fatty acid with double bonds between one of more pairs of successive carbon atoms will have fewer hydrogen atoms, thus making it unsaturated. 3) Polyunsaturated - Fatty acids with more than one double bond are called polyunsaturated. *Triglycerides contain 3 fatty acids.*

Relate position in the periodic table to atomic structure and the formation of ions.

*the elements exhibit a pattern of chemical properties that repeats itself in groups of 8.* The interactions between valence electrons are the basis for the differing chemical properties of elements. for most atoms that are essential to life, they contain no more than 8 electrons, and the chemical behavior of an element reflects how many of the eight positions are filled. elements with 8 electrons in their outer energy level are inert/ NONREACTIVE — and these elements are called the noble gases. elements with only 7 electrons in their outsr energy shell are highly reactive (because they need to gain an extra electron to fill their energy level.) elements with only one electron in their outsr energy level are also very reactive, but they tend to lose the one electron they have in their outer level. the more reactive the elements are, the more viable they are to create ions. both the far right and far left side of the periodic table are highly reactive (far left: less valence electrons, far right: more valence electrons) so they want to become stable.

1) explain what pH buffers do, 2) the mechanism by which they do it, 3) and why their function is important in living cells.

1) A buffer is a solution that can resist pH change upon the addition of an acidic or basic components. 2) It is able to neutralize small amounts of added acid or base, thus maintaining the pH of the solution relatively stable. This is important for processes and/or reactions which require specific and stable pH ranges. (You can add a base to a solution to neutralize some of the acid present, thus the pH rises.) 3) A small change in pH can change the shape of the enzyme, therefore disrupt enzymes' activities. for this reason, it is important that a cell maintain a constant pH level.

Describe 1) atomic structure, 2) the characteristics of subatomic particles, and 3) how they determine chemical properties

1) atomic structure - the atomic structure includes a central nucleus and orbiting electrons. every atom possesses an orbiting cloud of tiny subatomic particles called electronz (that move around the core.) at the center of each atom is a very small, dense nucleus formed of two other kinds of subatomic particles: protons (positive) and neutrons (no charge.) the only atom that doesnt have these traits is hydrogen, which usually only has one proton and no neutrons in its nucleus. 2) the characteristics of the subatomic particles: protons carry a positive charge, electrons carry a negative charge, and each neutron has no charge. 3) how protons/ neutrons/ electrons determine chemical properties: if an atom, such as sodium, loses an electron, it will be more positively charged — because electrons are negatively charged. if an atom such as chlorine gains an electron, it will be more negatively charged.

List the emergent properties of water that are important for biology, being able to describe the cause of each property and give examples of impacts on living organisms.

1) cohesion: explanation: hydrogen bonds hold water molecules together. benefit to life: leaves pull water upward from the roots, seeds swell and germinate 2) high specific heat: explanation: hydrogen bonds absorb heat when they break and release heat when they form, minimizing temperature changes. benefit to life: water stabilizes the temperature of organisms and the environment 3) high heat of vaporization: explanation: many hydrogen bonds must be broken for water to evaporate. benefit to life: evaporation of water cools body surfaces 4) lower density of ice: explanation: water molecules in an ice crystal are relatively far apart because of the hydrogen bonding. benefit to life: because ice is less dense than water, lakes do not freeze solid, allowing fish and other life in lakes to survive the winter 5) solubility: polar water molecules are attracted to ions and polar compounds, making these compounds soluble. benefit to life: many kinds of molecules can move freely in cells, permitting a diverse array of chemical reactions

Compare and contrast the different types of chemical bonds and interactions discussed, and what causes them.

The first type of bond discussed are ionic bonds — therefore, two elements put together (to make a compound.) Because it is charged, it is called "ionic." For example, sodium only has onr valence electron, and chlorine has 7 valence electrons. Due to the fact that they are opposites, theh attract. Chlorine wants to take that singular electron from sodium in order to complete it's first outer shell. (Sodium wants to lose the electron, and sodium wants to gain one in order to complete it's valence electron shell. The second type of bond discussed is called a covalent bond. Instead of "stealing electrons," as the ionic bond does, they share them — sharing electrons make it a covalent bond. For example, lets take 2 oxygen atoms — a neutral oxygen has 8 electrons total, but 6 of them are in it's outer shell. Therefore, there are 6 valence electrons. In order for the first atom to become stable, it would love to share electrons with the second oxygen atom. The second atom would also love to do the same, be ause they're both oxygen atoms with only 6 valence electrons. Therefore, each atom shares it's electrons with each other. Because of the shared electrons, the atoms stick together — which makes the atoms have a "covalent bond." Covalent bonds help with stability.

Predict how atoms such as C, H, O, and N share electrons in a covalent bond, the role of electronegativity, and the potential for hydrogen bonding between molecules.

The further right you go on the periodic table (with the exception of noble gasses, because they're not super reactive) the more electronegative each element is. Therefore, atoms C, H, O & N would most likely yearn to share their electrons in order to gain stability (AKA, they are more electronegative — because they want to "hog" electrons. The potential for hydrogen to bond between molecules is in the middle because it's electronegativity is in the middle. (?)

name and describe the most common disaccharides and polysaccharides found in nature, their primary functions in living organisms, the monomers that each are made of, and the bonds that join the monomers

most common disaccharides: 1) Sucrose 2) Maltose 3) Lactose (Monosaccharides make up each of these) most common polysaccharides: 1) glycogen 2) starch 3) cellulose Disaccharides primary functions/ where they're found in nature: 1) Sucrose: this is table sugar, and it is also what many animals/ humans eat. also, it is used by most plants to transport glucose. 2) Maltose: this is used in grain for storage. therefore, it is created in seeds/ other parts of a plant while they plant breaks down its stored energy. that energy is used to help the plant sprout. 3) Lactose - found in mammals, primarily. (breast milk). It is used for energy because it is technically milk sugar. Polysaccharides primary functions/ where they're found in nature: 1) Glycogen: (found in humans/ animals). "Glycogen is mainly stored in the liver and the muscles and provides the body with a readily available source of energy if blood glucose levels decrease." 2) Starch: found in plants. "The main function of starch is as way to store energy for plants. Starch is a source of sugar in an animal's diet." 3) Cellulose: "Cellulose is the main substance found in *plant cell walls* and helps the plant to remain stiff and strong." Monomers that make up each of them: 1) Sucrose - when glucose and fructose go through a *dehydration reaction*, sucrose (disaccharide) is formed. 2) Lactose - glucose and galactose go through dehydration reaction to make up lactose. 3) maltose: two glucose molecules go through a dehydration reaction to make maltose. (from a monosaccharide to a disaccharide) *monosaccharide to disaccharide: dehydration disaccharide to monosaccharide: hydrolysis*

predict whether a given molecule will dissolve easily in water

polar molecules and ions are soluble in water. water molecules gather closely around any substance that bears an electrical charge, whether the substance carries a full charge (ion) or a charge separation (polar molecule.) for example, table sugar is composed of molecules that contain polar hydroxyl (OH) groups. a sugar crystals dissolves rapidly in water because water molecules can form hydrogen bonds with individual hydroxyl groups of the sucrose molecules. therefore, sucrose (sugar) is soluble in water. every time a sucrose molecule dissociates or breaks away from a solid sugar crystal, water molecules surround it in a cloud, forming a *hydration shell* that prevents it from associating/ clumping back together with other sucrose molecules. hydration shells also form around *Na* and *Cl*.

describe what occurs during a chemical reaction, including the causes

the formation and breaking of chemical bonds, which is the essence of chemistry, is called a "chemical reaction." all chemical reactions involve the shifting of atoms from one molecule or ionic compound to another, without any change in the number or identity of the atoms. A chemical reaction is made up of reactants and products. 6H2O + 6CO2 —> C6H12O6 + 6O2 (reactants) (products) causes of chemical reactions: 1) temperature: heating the reactants increases the rate of a reaction because the reactants collide with one another more often. thus, care must be taken that the temperature is not so high that it destroys the molecules.) 2) concentration of reactants and products: reactions proceed more quickly when more reactants are available, allowing more frequent collisions. an accumulation of products typically slows the reaction and, in reversible reactions, may speed the reaction in the reverse direction 3) catalysts: a catalyst is a substance that increases the rate of a reaction. it doesn't alter the reactions equilibrium between reactants and products, but it does shorten the time needed to reach equilibrium, often dramatically. in living systems, proteins called "enzymes" catalyze almost every chemical reaction.

Define atomic number

the number of protons in the nucleus of an atom. "different atoms are defined by their atomic number, which is the number of protons. atoms w/ the same atomic number have the same number of protons, exhibit the same chemical properties, and are said to be the same element."

Draw and explain a labeled figure that relates the structure of individual water molecules to hydrogen bonding between molecules.

the polarity of water allows water momolecules to be attracted to one another — that is, water is cohesive. the oxygen end of each water molecule, which is partially negative, is attracted to the hydrogen end, which is partially positive. (opposites attract!) this attraction produces hydrogen bonds among water molecules. each hydrogen bond individually is very weak and transient, lasting on average only one-hundred billionth of a second. the cumulative effects of large numbers of these bonds, however, can become very large. water forms an abundance of hydrogen bonds, which are responsible for many of its important physical properties.