Biology: Learning Outcomes (Week 1-4)

Predict whether a given molecule will dissolve easily in water:

Water molecules gather around any substance that bears an electrical charge, whether that substance is a full charge (ion) or a charge separation (polar molecule). When a molecule dissolves in water individual ions break away from the molecule and become surrounded by water molecules in a cloud, forming a hydration shell that prevents it from associating with other sucrose molecules.

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:

- Dehydration reaction is the formation of monomers to polymers. They form a covalent bond between two monomers, a -OH group is removed from one monomer, and a hydrogen atom (H) is removed from the other, which is the same as the removal of a molecule of water. For every subunit added to a macromolecule, one water molecule is removed. - Hydrolysis reaction is the formation of polymers to monomers. Cells disassemble polymers into their constituent monomers by reversing the dehydration reaction - a molecule of water is added instead of removed. A hydrogen atom is attached to one subunit and a hydroxyl group to the other, breaking the covalent bond joining the subunits.

The seven characteristics:

1. Cellular organization: all organisms consist of one or more cells. Often too tiny to see, cells carry out the basic activities of living. Each cell is bounded by a membrane that separates it from its surroundings. 2. Ordered complexity: all living things are both complex and highly ordered. Your body is composed of many different kinds of cells, each containing many complex molecular structures. Many nonliving things may also be complex, but they do not exhibit this degree of ordered complexity. 3. Sensitivity: All organisms respond to stimuli. Plants grow toward a source light, and the pupils of your eyes dilate when you walk into a dark room. 4. Growth, development, and reproduction: All organisms are capable of growing and reproducing, and they all possess hereditary molecules that are passed to their offspring, ensuring that the offspring are of the same species. 5. Energy utilization: All organisms take in energy and use it to perform many kinds of work. Every muscle in your body is powered with energy you obtain from your diet. 6. Homeostasis: All organisms maintain relatively constant internal conditions that are different from their environment, a process called homeostasis. For example, your body temperature remains stable despite changes in outside temperatures. 7. Evolutionary adaptation: all organisms interact with other organisms and the nonliving environment in ways that influence their survival, and as a consequence, organisms evolve adaptations to their environment.

List five common misconceptions about evolution and explain what is wrong with each one:

1. Evolutionary theory implies that life evolved (and continues to evolve) randomly, or by chance. Chance and randomness do factor into evolution and the history of life in many different ways, however, some important mechanisms of evolution are non-random, and these make the overall process non-random. 2. Evolution results in progress; organisms are always getting better through evolution. One important mechanism of evolution, natural selection, does result in the evolution of improved abilities to survive and reproduce, however, this does not mean that evolution is progressive: natural selection does not produce organisms perfectly suited to their environments - evolutionary change is not always necessary for species to persist. 3. Individual organisms can evolve during a single lifespan. Evolutionary change is based on changes in the genetic makeup of populations over time. Populations, not individuals organisms evolve. 4. Evolution only occurs slowly and gradually. Evolution occurs slowly and gradually, but it can also occur rapidly. 5. Because evolution is slow, humans cannot influence it. Evolution sometimes occurs quickly, and since humans often cause major changes in the environment, we are frequently the instigators of evolution in other organisms.

Explain each of the five core concepts of biology:

1. Life is subject to chemical and physical laws: meaning it is important to emphasize that living systems operate according to known chemical and physical principles. 2. Structure determines function: meaning when we know the function of a particular structure, we can infer the function of similar structures found in different contexts, and if the structure is altered, function is disrupted, with potential physiological consequences. 3. Living systems transform energy and matter: meaning living systems have a constant need for energy in order to constantly transform energy and matter. 4. Living systems depend on information transaction: meaning cells acquire information about their environment, send and receive signals, and respond to all of this information with signal transduction systems that can change cell morphology, behavior, or physiology. 5. Evolution explains the unity and diversity of life: meaning all organisms alive today have descended from a simple cellular organism, in which the characteristics of that organism have been preserved through evolutionary history into the present, and the unity of life that we see in certain key characteristics shared by many related life-forms contrasts with the incredible diversity of living things in the varied environments on Earth.

Describe how Darwin's theory of evolution by natural selection works:

1. Variation: There's a variation in traits, some organisms have different physical traits. 2. Inheritance: There is a differential reproduction, since the environment can't support unlimited population growth, not all individuals get to reproduce to their full potential. 3. Selection: there is heredity, the surviving population have more offspring of the same traits that the organism expresses because this trait has a genetic basis. 4. Time: End result, the more advantageous trait (surviving organism), allows to have more offspring - if this process, continues, eventually, all individuals within the population will become the organism with the advantageous trait.

Explain what pH buffers do, the mechanism which they do it, and why their function is important in living cells:

A buffer is a substance that resists changes in pH. Buffers act by releasing hydrogen ions when a base is added and absorbing hydrogen ions when acid is added, with the overall effect of keeping hydrogen ions relatively constant close to neutral, 7. Most enzymes in living systems are extremely sensitive to pH, and often even a small change in pH will alter their shape, thereby disrupting their activities. Within organisms, most buffers consist of pairs of substances, one an acid and the other a base. The key buffer in human blood is an acid-base pair consisting of carbonic acid (acid) and bicarbonate (base). These two substances interact in a part of reversible reactions. First, carbon dioxide and water join to form carbonic acid, which in a second reaction dissociates to yield bicarbonate ion and hydrogen ion. If some acid or other substance adds hydrogen ions to the blood, bicarbonate ion acts as a base and removes the excess hydrogen ions by forming bicarbonate. Similarly, if a basic substance removes hydrogen ions from the blood, bicarbonate ion dissociates, releasing more hydrogen ions into the blood (carbonic acid).

Describe what occurs during a chemical reaction, including the causes:

A chemical reaction is the formation and breaking of chemical bonds. 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. The original molecules before a reaction starts as reactants, and the molecules resulting from the chemical reactions are products. The extent to which chemical reactions occur is influenced by three important factors: temperature (heating the reactants increases the rate of a reaction because the reactants collide with one another more often), 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), and catalysts (a catalyst is a substance that increases the rate of the reaction - it doesn't alter the reactions equilibrium between reactants and products, but it does shorten the time needed to reach equilibrium).

Define compound:

A compound is when a molecule contains atoms of more than one element.

List the structures that all cells have, describing the composition and function of each of these structures:

All cells contains DNA for genetic material and contains the genes that code for the proteins synthesized by the cell. All cells contain a semifluid (jell-o)matrix called the cytoplasm that fills the interior of the cell that contains all of the sugars, amino acids, and proteins the cell uses to carry out its everyday activities. All cells have ribosomes that are composed of RNA and protein that synthesize all cellular proteins, and they use information from the genome and other accessory molecule to direct the synthesis of proteins by sequential addition of amino acids. All cells contain plasma membrane which encloses a cell and separates its contents from its surroundings, and the proteins of the plasma membrane are generally responsible for a cell's ability to interact with the environment.

Describe the defining characteristics of all living organisms:

All living organisms respond to stimuli, and are capable of growing and reproducing, and they all possess hereditary molecules that are passed to their offspring. All living organisms take in energy and use it to perform many kinds of work, they maintain relatively constant internal conditions that are different from their environment, and they all interact with other organisms and the nonliving environment in ways that influence their survival and or able to evolve adaptions to their environment.

Draw a diagram showing how proteins are constructed from monomers, labeling the bond that joins them together:

Amino acids are the monomers of proteins. When two amino acids, a positive amino end (+) and one negative carboxyl end (-) group together, they undergo a dehydration reaction to form a covalent bond - the covalent bond that links two amino acids is called a peptide bond. The two amino acids linked by such a bond are not free to rotate around the N - C linkage because the peptide bond has a partial double-bond character.

Define element:

An element is defined as any substance that cannot be broken down to any other substance by ordinary chemical means.

Define isotope:

An isotope is atoms of a single element that possess different numbers of neutrons than their protons.

Define atomic mass:

Atomic mass is the number is refers to the sum of the masses of its protons and neutrons.

Define atomic number:

Atomic number is the number of protons within an atom.

Describe atomic structure, the characteristics of subatomic particles, and how they determine chemical properties:

Atomic structure includes an orbiting cloud of tiny subatomic particles called electrons whizzing around a core, and at the center of each atom is a small, very dense nucleus formed of two other kinds of subatomic particles: protons and neutrons. Each proton carries a positive (+) charge, each neutron has no charge, and each electron carries a negative (-) charge. Typically, an atom has one electron for each proton and is thus electrically neutral. The chemical behavior of an atom is due to the number and configuration of electrons. An atom having more protons than electrons has a net positive charge called a cation, and an atom having fewer protons than electrons carries a net negative charge called an anion.

Define biological evolution:

Biological evolution is descent with inherited modification.

Describe what chaperonins do, how they do it, and why their function is important:

Chaperone proteins accompany a protein on its path to a properly folded state. Many are so-called heat shock proteins, produced in large amounts in response to elevated temperature. High temperatures cause proteins to unfold, and heat shock chaperone proteins help the cell's proteins to refold properly. Chaperonins associate to form a large macromolecular complex that resembles a cylindrical container. Proteins can move into the container, and the container itself can change its shape considerably. Experiments have shown that an improperly folded protein can enter the chaperonin and be refolded - it seems to involve changes in the hydrophobicity of the interior of the chamber. We tend to think of proteins as being fixed structures, but this is clearly not the case for chaperonins and this flexibility is necessary for their function.

Describe the impact of compartmentalization on eukaryotic cells, including the structures that allow eukaryotes to achieve this compartmentalization:

Compartmentalization allows the eukaryotic cell to have multiple membrane-bound organelles, usually specialized for a particular function and containing specific proteins, create compartments in the cytoplasm and also increases the surface area of the cell. Compartments include plasma membrane cell wall, mitochondria, chloroplast, and among others.

Describe how DNA and RNA molecules store information:

DNA: Organisms use sequences of nucleotides in DNA to encode information specifying the amino acid sequences of their proteins. Thus, DNA stores biological information in sequences of four bases of nucleic acid: adenine (A), thymine (T), cytosine (C) and guanine (G), which are strung along ribbons of sugar-phosphate molecules in the shape of a double helix. RNA: RNA copies DNA (produced by transcription) and it carries the information in the form of mRNA, it is part of the ribosome, in the form of ribosomal RNA (rRNA), and it carries amino acids in the form of transfer RNA (tRNA).

Describe Darwin's theory of evolution by natural selection:

Darwin's theory is that evolution occurs because of natural selection.

Define denaturation, describe what can cause it, and what its impacts are:

Denaturation is when the protein's environment is altered, the protein may change its shape or even unfold completely. Proteins can be denatured when the pH, temperature, or ionic concentration of the surrounding solution changes. Denatured proteins are usually biologically inactive - this action is particularly significant in the case of enzymes. Because practically every chemical reaction in a living organism is catalyzed by a specific enzyme, it is vital that a cell's enzymes work properly.

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

Discrete levels correspond to the specific amount of energy electrons have within the atom. Every atom exhibits a ladder of potential energy values, a discrete set of orbitals at particular energetic "distances" from the nucleus. Because the amount of energy an electron possesses is related to its distance from the nucleus, electrons that are the same distance from the nucleus have the same energy, even if they occupy different orbitals. The energy levels are denoted with letters K, L, M, and so on. When an atom absorbs energy, an electron moves to a higher energy level, farther from the nucleus, when an electron falls to lower energy levels, closer to the nucleus, energy is released.

Draw a labeled picture that shows the components of chromatin and how it and DNA are organized into eukaryotic chromosomes:

Each chromosome consists of a single DNA molecule. These must be compacted to fit into the cell nucleus. The DNA duplex is wound around proteins called histones to form nucleosomes. These appear as "beads on a string" because of their appearance in an electron microscope. The nucleosomes are further coiled into higher-order structures for further compaction, that appear to involve organized chromatin loops. The precise organization of mitotic chromosomes is unknown, but the figure shows one arrangement of many possibilities.

Define science:

Science is developing an increasingly accurate understanding of the world around us using observation and reasoning.

Draw each of the common functional groups found in organic molecules and list the types of macromolecules that they are each found in:

Hydroxyl: carbohydrates, proteins, nucleic acids, lipids Carbonyl: carbohydrates, nucleic acids Carboxyl: proteins lipids Amino: proteins, nucleic acids Sulfhydryl: proteins Phosphate: nucleic acids Methyl: proteins, nucleic acids

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

If all of the internal carbon atoms in a fatty acid chain are bonded to two hydrogen atoms, we call this saturated, with the maximum number of hydrogen atoms possible. A fatty acid with double bonds between one or more pairs of successive carbon atoms will have fewer hydrogen atoms, and is thus unsaturated. Fatty acids with one double bond are called monounsaturated, and those with more than one double bond are termed polyunsaturated.

List and describe the different monomers that make up nucleic acids, the three components they all contain, and the two different groups each base is placed into. Draw a cartoon version (no need to draw every atom, just the important distinguishing and functional features) of each nucleotide:

Nucleic acids consist of long polymers of repeating subunits called nucleotides. Each nucleotide consists of three components: a 5-carbon sugar, a phosphate group, and an organic nitrogen-containing base. In DNA, the sugar is deoxyribose and in RNA it is ribose. Nucleotides have five types of nitrogenous bases. Two of these are large, double-ring molecules called purines that are each found in both DNA and RNA; the two purines are adenine (A) and guanine (G). The other three bases are single-ring molecules called pyrimidines that include cytosine (C) in both DNA and RNA, thymine (T) in DNA only, and uracil (U) in RNA only.

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

Ionic bonds form when atoms with opposite electrical charges (ions) attract. The way ionic bonds stick to each other is for example if sodium has one valence electron, and chlorine has 7 valence electrons, and in order for chlorine to complete its outer shell it will pull the electron from sodium element. Sodium will lose an electron and chlorine will gain an electron, resulting in sodium becoming positively charged, and chlorine becoming negatively charged, and thus become attracted to each other. Covalent bonds form when two atoms share one or more pairs of valence electrons. For example two oxygen atoms, a neutral oxygen has eight electrons in total, but six valence electrons are in its outer shell. There are two valence electrons that are not paired with another electron, and in order to become more stable, it needs to share the two electrons with the other oxygen atom causing these two oxygen atoms to stick together and become more stable.

Give a definition of life:

Life is a living organism that consists of one or more cells that carry out basic activities for living and of which is composed of many different kinds of cells that each contain many complex molecular structures.

Draw the basic molecular structure of triglycerides, steroids, and phospholipids. Describe what chemical structures are the same for lipids within each group and which vary:

Like triglycerides, phospholipids have a glycerol backbone, but unlike triglycerides, phospholipids only have two fatty acid molecules attached to the glycerol backbone, while the third carbon of the glycerol backbone is bonded to a phosphate group. Unlike phospholipids, steroids have a fused ring structure, although they do not resemble the other lipids, they are grouped with them because they are also hydrophobic and insoluble in water.

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

Lipids are energy storage (fats and oils), and are defined group of molecules with one main chemical characteristic: they are insoluble in water. One type of lipid is phospholipids which are the most important molecules of the cell because they form the core of all biological membranes. Another type of lipid is steroids, which help cell membranes contain the steroid cholesterol, and other functions such as hormones in multicellular animals. Another type of lipid is triglycerides and the primary function of triglycerides is energy storage, and they are obtained via the food that we eat.

Describe the factors that limit cell size:

Most cells are relatively small for reasons related to the diffusion of substances into and out of them. The rate of diffusion is affected by a number of variables, including (1) surface area available for diffusion, (2) temperature, (3) concentration gradient of diffusing substance, and (4) the distance over which diffusion must occur. As the size of a cell increases, the length of time for diffusion from the outside membrane to the interior of the cell increases as well. The advantage of small cell size is readily apparent in terms of the surface area-to-volume ratio. As a cell's size increases, its volume increases much more rapidly than its surface area. Because small cells have more surface area per unit of volume than large ones, control over cell contents is more effective when cells are relatively small.

Describe what protein motifs and domains are, and how they relate to protein structure and function:

Motifs are similarities between otherwise dissimilar proteins, and they are useful in determining the function of unknown proteins - the sequence of an unknown protein can be compared to a database of known functional motifs. Finding a characterized motif in an unknown protein can shed light on that protein's function. Domains of proteins are functional units within a larger structure within the tertiary structure of a protein. Most proteins are made up of multiple domains that perform different parts of the protein's function - in many cases, these domains can be physically separated. These functional domains of proteins may also help the protein fold into its proper shape - as a polypeptide chain folds, the domains take their proper shape, each more or less independently of the others.

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

One common disaccharide is when glucose forms a disaccharide with the structural isomer fructose, the resulting disaccharide is sucrose, which sucrose is the form most plants use to transport glucose and is the sugar that most humans and other animals eat. Another common disaccharide is when glucose forms a disaccharide with the stereoisomer galactose, the resulting disaccharide is lactose, which many mammals supply energy to their young in the form of lactose and of which is mostly reserved for offspring. Another common disaccharide is maltose that is composed up of alpha glucose molecules, in which organisms use as a source of energy so that hydrolysis of the disaccharide maltose comes in the form of simple sugar glucose when enzymes catalyze. One common type of polysaccharide is starch, which is a storage polysaccharide that consists of alpha glucose molecules linked in long chains, which provide energy storage. Another common type of polysaccharide is cellulose, a structural polysaccharide, also consisting of glucose molecules linked in chains, but these molecules are beta glucose molecules, which also works as a biological structural material for some animal. Another common type of polysaccharide is chitin, a structural material, of which is a nitrogen-containing derivative of glucose, in which it forms a tough, resistant surface material that serves as the hard exoskeleton of insects and crustaceans.

Give example how isotopes can be used in biological research and medicine:

One example of how isotopes can be used in biological research is radiation in radioisotopes is useful in treating certain types of illnesses, particularly cancerous tumors, and are essential parts of medical diagnostic procedures for treatment, another example would be using half-life in the carbon dating of fossils and other materials to accurately determine when these materials formed.

List the basic cellular characteristics that distinguish between prokaryotic and eukaryotic cells:

Prokaryotic cells are smaller cells that lack any membrane-bounded organelles, such as a nucleus - instead a single circular molecule of DNA that is found near the center of the cell in an area called the nucleoid. Prokaryotes strength and shape of the cell is determined by the cell wall and not these cytoskeletal elements (actin and tubulin), however, cell wall structure is influenced by the cytoskeleton. Eukaryotic cells are the hallmark of compartmentalization - this is achieved through a combination of an extensive endomembrane system that weaves through the cell interior and by numerous organelles. These organelles include membrane-bounded structures that from compartments within which multiple biochemical processes can proceed simultaneously and independently. The largest and most easily seen organelle within a eukaryotic cell is the nucleus in which is bounded by two phospholipid bilayer membranes which together make up the nuclear envelope.

Identify and draw the basic structure that all amino acids share:

Proteins are linear polymers made with 20 different amino acids. Amino acids contain an amino group (-NH2) and an acidic carboxyl group (-COOH) which are bonded to a central carbon atom, with an additional hydrogen and a functional side group indicated by R. These components completely fill the bonds of the central carbon.

How is science different from other ways of knowing and understanding the world around us:

Science is different because it is expressing ideas of which we are most certain and are accepted as a general principle or body of knowledge, which can always be checked and even adjusted based on new information or findings that can express the idea even more accurately. Based on this, we can trust that science is the most important channel of knowledge because human error is rarely of occurrence with the constant retesting of hypotheses and experiments and adjustments to these in an effort to make the results more accurate.

What is science useful for:

Science is useful because it holds on of the most important channels of knowledge, it generates solutions for everyday life and helps us get a better understanding of the mysteries this world holds.

Explain the nature of acids and bases, and their relationship to the pH scale:

The concentration of hydrogen ions, and concurrently of hydroxide ions, in a solution is described by the terms acidity and basicity. The pH scale is a more convenient way to express the hydrogen ion concentration of a solution. Pure water has a pH of 7, which is considered to be neutral - neither acidic nor basic. Solutions with a pH less than 7 are acidic, whereas those with a pH greater than 7 are basic. The scale is logarithmic, which means that a pH change of 1 represents a 10-fold change in the concentration of hydrogen ions. Example: a solution with a pH of 4 therefore has 10 times the hydrogen ions of a solution with a pH of 5 and 100 times the hydrogen ions of a solution with a pH of 6.

List the different groups of amino acids and be able to place an amino acid into the appropriate group based on its R-group:

The different groups of amino acids are nonaromatic groups, aromatic groups, and special function groups. Seven amino acids are nonpolar because they have -CH2 or -CH3 in their groups; two of the seven contain ring structures with alternating double and single bonds, which classifies them also as aromatic. Another five are polar because they have oxygen or a hydroxyl group in their R groups. Five other are capable of ionizing to a charged form. The remaining three special-function amino acids have chemical properties that allow them to help form links between protein chains or kinks in proteins.

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:

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

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 the more electronegativity increases in the elements C, H, O, and N, causing them to want to attach to the electrons they are sharing, making these elements have a slight negative charge. The shared electrons are more likely to be closer to the atom with greater electronegativity, and less likely to be near the atom of lower electronegativity. Regions of partial negative charge near the more electronegative atom, and regions of partial positive charge near the less electronegative atom. The potential for hydrogen bonding between two hydrogen atoms are the affinity for electrons are the same and the electrons are equally shared, making the bonds nonpolar.

Describe the structure and function of the eukaryotic nucleus, nucleolus, and DNA within the nucleus:

The largest and most easily seen organelle within a eukaryotic cell is the nucleus, which are typically located in the central region of the cell. The nucleus contains the genetic information that enables the synthesis of nearly all proteins of a living eukaryotic cell. The surface of the nucleus is bounded by two phospholipid bilayer membranes, which together make up the nuclear envelope. Many nuclei exhibit a dark-staining zone called the nucleolus, which is a region where intensive synthesis of ribosomal RNA is taking place. In eukaryotes, the DNA is divided into multiple linear chromosomes, which are organized with proteins into a complex structure called chromatin. Chromatin is also more organized in the nucleus than was once thought and the state of the DNA in chromatin must also change over the course of cell division. Chromosomes become compacted into a more highly condensed state that forms the X-shaped chromosomes visible in the light microscope.

List the most 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:

The most common monosaccharides are 3-carbon (CH₂O)₃, Sugar, 5-carbon Sugars (CH₂O)₅, and 6-carbon sugars (CH₂O)₆.

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

The periodic table is based on the interactions of the electrons in the outermost energy level of the different elements (valence electrons), and their interactions are the basic for the differing chemical properties of elements, along with the chemical behavior of an element reflecting how many of the eight positions are filled. Elements with eight electrons in their outer energy level are inert or nonreactive, and elements with only seven electrons in their outer energy level are highly reactive. They tend to gain the extra electron needed to fill the energy level. Elements with only one electron in their outer energy level are also very reactive, but they tend to lose the single electron in their outer level.

Discuss why protein structure is important. List and discuss the different levels of structure and what chemical mechanism(s) determine(s) each level of structure:

The shape of a protein determines its function. Primary structure: amino acid sequence. Because the R groups that distinguish the amino acids play no role in the peptide backbone of proteins, a protein can consist of any sequence of amino acids. Secondary structure: hydrogen bonding pattern. The amino and carboxyl groups could interact with one another if the peptide was coiled into a spiral called the alpha helix, and another form can occur between regions of peptide aligned next to each other to form a planar structure called a beta sheet. Tertiary structure: folds and links. A protein is initially driven into its tertiary structure by hydrophobic exclusion from water, ionic bonds between oppositely charge R groups bring regions into close proximity, and disulfide bonds (covalent links between two cysteine R groups) lock particular regions together. Quaternary structure: subunit arrangements. When two or more polypeptide chains associate to form a functional protein, the individual chains are referred to as subunits of the protein. In proteins composed of subunits, the interfaces where the subunits touch one another are often nonpolar.

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

The shape of a water molecule has two covalent bonds that have a partial charge at each end: delta - at the oxygen end and delta + at the hydrogen end. The most stable arrangement of these charges is a tetrahedron, in which the two negative and two positive charges are approximately equidistant from one another with the oxygen atom at the center of the tetrahedron. This arrangement of partial charges allows water molecules to interact forming weak chemical associations called hydrogen bonds. The partially negative delta - O atom in one molecule is attracted to the partially positive delta + H atoms of other water molecules. Hydrogen bonding is not limited to water molecules. Any molecule with H attached to a more electronegative atom, usually oxygen (O) or nitrogen (N), can potentially form hydrogen bonds.

Name the two types of nucleic acids and describe how they differ in structure, monomer composition, and function:

The two types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The function of DNA is to store (genetic) information, and the function of RNA plays a variety of roles in the cell, such as, short-lived copies of genetic information used to direct the synthesis of proteins and it can also function to regulate the process of gene expression. The monomer composition of DNA is nucleotides, which have three components: 5-carbon sugar (deoxyribose), a phosphate group, and an organic nitrogen-containing base. The monomer composition of RNA is nucleotides, which have three components: 5-carbon sugar (ribose), a phosphate group, and an organic nitrogen-containing base.