AP Biology Exam Review Unit 1

What is the structure of an amino acid?

All amino acids share a common structure; the general formula for an amino acid contains an amino group (NH2), a carboxyl group (COOH), a variable R group (side chain), and a hydrogen atom all centered around an alpha carbon.

Identify three environmental conditions that can alter protein structure.

An alteration in salt concentration, temperature, pH, and other aspects of a protein's environment (such as chemicals that disrupt the hydrogen bonds, ionic bonds, or disulfide bridges that maintain a protein's shape, excessive heat, and more) can potentially cause the weak chemical bonds and interactions within the molecule to be destroyed—the unraveling of a protein, where it loses its native shape and subsequently its function, is called denaturation.

Using the properties of water, describe how water can move up a capillary tube to move from the roots to the leaves in a plant.

Cohesion due to hydrogen bonding contributed to the transport of water and dissolved nutrients against gravity in plants. Water from the roots reached the leaves through a network of water-conducting cells; as water evaporates from a leaf, hydrogen bonds cause water molecules leaving the veins to tug on molecules farther down, and the upward pull is transmitted through the water-conducting cells all the way to the roots.

What are three properties of water?

Cohesive behavior, the ability to moderate temperature, and expansion upon freezing.

Where are hydrogen bounds found in DNA? How many hydrogen bonds are found between each complementary base pairing?

In DNA, hydrogen bonds exist between the opposing bases of complementary base pairs. This means that adenine (A) in one strand opposes thymine (T) in the other strand, and guanine (G) opposes cytosine (C). The A-T pair forms two hydrogen bonds, while the C-G pair forms three.

How does hydrogen bonding allow for expansion upon cooling in water?

Water is one of the few substances that are less dense as a solid than as a liquid, meaning that ice floats on water. Instead of contracting and becoming denser as it solidifies, water expands; as water begins to freeze (as the temperature falls from 4°C to 0°C), more and more if it's molecules are moving too slowly to break hydrogen bonds and become locked into a crystalline lattice (each water no like is hydrogen-bonded to four partners).

What are the elements found in a carbohydrate? How are carbohydrates structured?

carbon (C), hydrogen (H), and oxygen (O) — monosaccharides generally have molecular formulas that are some multiple of the unit CH2O and that contain a carbonyl group and multiple hydroxyl groups. The carbon skeleton of a sugar molecule can range from three to seven carbons long (six=hexoses, three=trioses, five=pentoses)

How does hydrogen bonding allow for cohesive behavior in water?

At any given moment, many of the molecules in liquid water are linked by multiple hydrogen bonds, which collectively hold the substance together and make water more structured than other liquids. This allows for adhesion (the clinging of one substance to another) and a relatively high surface tension (a measure of how difficult it is to stretch or break the surface of a liquid).

Using the properties of water, describe how a water strider can walk on water.

The hydrogen bonds in water give it an unusually high surface tension, making it behave as though it were coated with an invisible film. A water strider can take advantage of water's resistance to surface breakage in order to walk across it.

What is a polymer?

A long molecule consisting of many similar or identical repeating building blocks (monomers) linked by covalent bonds.

What is the significance of the structure of adenosine triphosphate (ATP)?

A more complicated organic phosphate, ATP consisted of an organic molecule called adenosine attached to a string of three phosphate groups. Where three phosphates are present in series, as in ATP, one phosphate may be split off as a result of a reaction with water. Having lost one phosphate, ATP becomes adenosine diphosphate, or ADP.

What is a phospholipid? Why are they essential for cells?

A phospholipid is a lipid that has a phosphate group attached to the glycerol and only two fatty acid chains instead of three; the third hydroxyl group of glycerol joins to a phosphate group and creates a negative charge, and can also be linked to additional small molecules. Phospholipids are a prime example of how form fits function on the molecular level, as they are major constituents of cell membranes and the existence of cells relies on the properties of phospholipids; the hydrocarbon tails are hydrophobic and are excluded from water while the phosphate group forms a hydrophilic head that has an affinity for water. When they are added to water, they self-assemble into double layered structure called "bilayers" that shield the hydrophobic tails from water. This forms a boundary between the cell and the external environment.

What is an organic compound?

Any compounding containing the element carbon (C), generally containing hydrogen (H) atoms as well.

What are the four macromolecules?

Carbohydrates, lipids, proteins, nucleus acids

What are the elements found in a lipid? How are lipids structured?

Carbon (C), hydrogen (H), and oxygen (O) — they generally consisted of mostly hydrocarbon regions

What helps to facilitate the chemical mechanisms by which cells make and break down polymers?

Enzymes (specialized macromolecules, usually proteins, that speed up chemical reactions)

What are hydrocarbons and where can they be found?

Hydrocarbons are organic molecules consisting of only carbon and hydrogen. They are a major component of petroleum (they can undergo reactions that release a relatively large amount of energy) and they are a major component in fats (hydrocarbon tails).

What is a lipid?

Lipids are the one class of large biological molecules that does not include true polymers and they are generally not big enoguh to be considered macromolecules. The compounds are grouped together because they are all nonpolar molecules with hydrophobic tendencies because of their structure (that mostly consists of hydrocarbon regions) and they make up fats, steroids and phospholipids (as well as waxes and pigments).

What are three functions of lipids in living organisms?

Lipids store energy, insulate body, and cushion and protect organs

What are the elements found in nucleic acids? What are parts found in all nucleotides? How are nucleic acids structured?

Nucleic acids contain Hydrogen (H), Oxygen (O), Nitrogen (N), Carbon (C), and Phosphorus (P). Nucleic acids are composed of a nitrogenous base (adenine, thymine in DNA, uracil in RNA, cytosine, and guanine), a five-carbon pentose sugar (deoxyribose in DNA, ribose in RNA), and one to three phosphate groups. There are two families of nitrogenous bases: pyrimidines (a molecule with one six-membered ring of carbon and nitrogen atoms, including cytosine, thymine, and uracil) and purines (a molecule with a six-membered ring fused to a five-membered ring, including adenine and guanine). In a polynucleotide, adjacent nucleotides are joined by a phosphodiester linkage that consists of a phosphate group that covalently links the sugars of the two nucleotides. This bonding results in sugar-phosphate backbone with two free ends that are distinctly different from each other. One end has a phosphate attached to a 5' carbon (the 5' end) and the other has a hydroxyl group attached to a 3' carbon (the 3' end). The sequence of bases along a DNA or mRNA polymer is unique for each gene (a discrete unit of inheritance) and provides very specific information to the cell. DNA molecules have two polynucleotide "strands", forming a double helix that run in opposite 5'—3' directions from each other (referred to as antiparallel). RNA, by contrast, exist as single strands.

What is the function of nucleic acids?

Nucleic acids store, transmit, and help express hereditary, or genetic, information. DNA provides directions for its own unique replication and directs RNA synthesis and controls protein synthesis through RNA in the process of gene expression. DNA is not directly involved in running the operations of the cell. A given gene along a DNA molecule can direct synthesis of a type of RNA called messenger RNA (mRNA), which interacts with the cell's protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein. Transfer RNAs (tRNA) function at specific sites in the ribosome during translation, which is a process that synthesizes a protein from an mRNA molecule. Ribosomal RNAs (rRNA) catalyze the assembly of amino acids into protein chains.

What are storage polysaccharides? What are examples of them?

Both plants and animals store sugars for later use. Plants (and humans with the help of enzymes) store starch (a polymer of glucose monomers) as granules within cells; synthesizing starch enables the plant to stockpile surplus glucose to be later withdrawn from the "bank" by hydrolysis (which breaks the bonds or glucose molecules) as a nutrient for cells. Most glucose monomers in starch are joined by 1-4 linkages and the simplest form of starch, amylose, is unbranched. Animals also store a polysaccharide called glycogen (a polymer of glucose that is like amylopectin (a more complex starch with 1-6 linkages) but more extensively branched), which is generally stored in liver and muscles to accommodate for times when the demand for sugar meant to sustain an animal for about a day before being replenished through eating.

What are carbohydrates?

Carbohydrates consist of sugars and polymers of sugars. The simplest carbohydrates are the monosaccharides (simple sugars), which are monomers from which more complex carbohydrates are built. Disaccharides are double sugars, consisting of two monosaccharides joined by a covalent bond (glycosidic linkage). Carbohydrates also include macromolecules called polysaccharides, polymers composed of many sugar building blocks joined together by dehydration synthesis.

What are the elements found in a protein? What are the functional groups found in all amino acids? How are proteins structured?

Carbon (C), oxygen (O), hydrogen (H), and nitrogen (N) are found in proteins. An amino acid group and a carboxyl group are both found in all amino acids. The specific activities of proteins result from their intricate three-dimensional architecture, the simplest level of which is the sequence of their amino acids. A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape; this specific structure determines how it works. All proteins share three superimposed levels of structure—primary (it's sequence of amino acids), secondary (segments of polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein's overall shape), and tertiary (the overall shapes of a polypeptide resulting from interactions between the side chains of the various amino acids) structure. A forth level, quaternary (the overall protein structure that results form the aggression of the polypeptide subunits) structure, arises when a protein consists of toe ore more polypeptide chains. When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group to the other, they can become joined by a dehydration reaction—the resulting covalent bond is called a peptide bond, and the repeated process yields a polypeptide.

Why is carbon so special compared to other elements?

Carbon is unparalleled in its ability to form molecules that are large, complex, and varied, as its atoms have four valence electrons (6 electrons total—2 in the first shell and 4 in the second shell) and can hold up to 8 electrons and form up to quadruple bonds to form a lot of different structures.

What are the three options for the R group? For each R group option, describe the polarity and justify your response.

1. Hydrophilic amino acids, with a charged or polar and uncharged R group (Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline) 2. Hydrophobic amino acids, with an aliphatic or bulky and aromatic R group (Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine) 3. Electrically charged side chains that are hydrophilic (Aspartic Acid, Glutamic Acid, Lysine, Arginine, Histidine) Water is a dipole and acts like a magnet, with the oxygen end having a negative charge and the hydrogen end having a positive charge. These charged ends can attract other polar molecules.

What are four functions of carbohydrates in living organisms?

1. Provide energy: Cells extract energy from glucose by breaking them down in a series of reactions called cellular respiration (the carbon skeletons serve as raw materials for the synthesis of other small organic molecules and sugars not used in these ways are generally incorporated as monomers into disaccharides and polysaccharides). 2. Build macromolecules: Sugar molecules that are not immediately used to provide and store energy are generally incorporated as monomers on disaccharides or polysaccharides. 3. Structure (building material): Organisms build strong materials from structural polysaccharides. 4. Storage material: Both plants and animals store sugars for later use.

What is an aqueous solution? Why is water considered the universal solvent?

An aqueous solution is one in which the solute is dissolved in water; water is the solvent. Water is a very versatile solvent due to the polarity of the molecule. Water is capable of dissolving ionic compounds such as salt (by surrounding individual ions with molecules of opposing charges to separate and shield them from one another) and polar molecules like sugars (by surrounding each of the solute molecules and form hydrogen bonds with them). Such (biological) molecules include blood, plant sap, and cellular liquid. Basically, it considered a universal solvent because almost anything dissolves in it, and because it dissolves more substances than any other solvent.

What are the functions of proteins?

Control the rate of reactions (speed them up, Regulate cell processes, used to form bones and muscles, transport substances into and out of the cell, help fight diseases. - Enzymatic proteins are responsible for selective acceleration of chemical reactions (i.e. digestive enzymes). - Defensive proteins are responsible for protecting against disease (i.e. antibodies). - Storage proteins are responsible for storage of amino acids (i.e. Casein). - Transport proteins are responsible for transport of substances (i.e. Hemoglobin). - Hormonal proteins are responsible for the coordination of an organism's activities (i.e. Insulin). - Receptor proteins are responsible for the response of a cell to chemical stimuli (i.e. membrane receptors). - Contractile proteins are responsible for movement (i.e. motor proteins, actin, myosin). - Structural proteins are responsible for support (i.e. Keratin and Collagen).

What is a fat? Why are the hydrophobic? How is a fat structured? What is the difference between a saturated fat and an unsaturated fat? What is the major function of fats?

Fats are large lipids that are constructed from two kinds of smaller molecules by dehydration reactions: glycerol (an alcohol with three carbons that bear a hydroxyl group) and fatty acids (a molecule bearing a long carbon skeleton, generally consisting of 16-18 carbon atoms with a carboxyl group at one end). The relatively nonpolar C—H bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic, as fats separate from water because the water molecules hydrogen bond to one another and exclude fats. In making a fat, three fatty acid molecules are each joined to glycerol by an ester linkage, a bond between a hydroxyl group and a carboxyl group; this results in a triacylglycerol that consists of three fatty acids linked to one glycerol. The terms saturated fats and unsaturated fats refer to structure of the hydrocarbon chains of the fatty acids. If there are no double bonds between carbon atoms composing the chain, then many hydrogen atoms are bonded to the skeleton; hence, the chain is saturated with hydrogen and referred to as saturated. (solid at room temperature with tightly packed fats) An unsaturated fatty acid has one or more double bonds, so fewer hydrogens can attach since it creates a kink (liquid at room temperature since they are not tightly packed). The major function of fats is energy storage.

Where are hydrogen bonds found in water?

Hydrogen bonds are located in between different water molecules, connecting the partial positive charge of one of the hydrogen atoms from one water molecule to the partial negative charge of the oxygen molecule of another water molecule.

What are isomers? What are the three types of isomers and what are their characteristics?

Isomers are compounds that have the same numbers of atoms of the same elements but different structures, and hence different properties. 1. Structural Isomers differ in the covalent arrangements of atoms or in the location of double bonds—the number of isomers increases tremendously as skeletal size increases. 2. Cis-trans Isomers different in spatial arrangements due to inflexibility of double bonds (they don't rotate like singles)—cis is in the same side while trans is on the opposite. 3. Enantiomers differ in shape due to the presence of an asymmetric carbon (one that is attached to four different atoms or groups of atoms). They are, in a way, left-handed and right-handed versions of the molecule.

What are nucleic acids? What are the nucleic acids?

Nucleic acids are polymers made of monomers called nucleotides; the two types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and they enable living organisms to reproduce their complex components form one generation to the next.

What is a hydrogen bond?

One of the weak chemical bonds that are central to the chemistry of life; a hydrogen bond is characterized by the non-covalent attraction between a hydrogen and an electronegative atom. When a hydrogen atom is covalently bonded to an electronegative atom, the hydrogen atom has a partial positive charge that allows it to be attracted to a different electronegative atom nearby. Typically, it is attracted to nitrogen or oxygen.

What are proteins?

Proteins are instrumental macromolecules that account for nearly every dynamic function of a living being and are made up of amino acid chains. They are biologically functional molecules made up of one or more polypeptides folded and coiled into a specific three-dimensional structure.

What are steroids? What is an example of a steroid?

Steroids are lipids characterized by carbon skeleton made up of four fused rings that are distinguished by the particular chemical groups attached to the ensemble of rings. Cholesterol is a crucial steroid for animals, as it is a common component of cell membranes and is the precursor from which other steroids (like vertebrate sex hormones) are synthesized.

What are structural polysaccharides? What are examples of them?

Structure (building material): Organisms build strong materials from structural polysaccharides, such as cellulose (one of the most abundant compounds on Earth that is produced by pants a major component of the tough walls that enclose plant cells). It is composed of 1-4 glycosidic linkages (varying from starch in ring structure, as starch uses the Alpha ring structure while cellulose uses the Beta), making it a non-helical and non-branched molecule with freely hydrogen-bonded hydroxyls (parallel cellulose molecules held together in this war are grouped in strong building units called microfibrils, which are important to paper and cotton. Enzymes that digest starch can only digest specific structures of linkages (Alpha enzymes cannot digest Beta enzymes), so cellulose abraded the wall of the digestive tract and stimulates the lining to secrete mucus and contributes to the smooth passage of food. Herbivores harbor cellulose-digesting prokaryotes (microbes that hydrolyze and convert the cellulose into nourishment). Chitin is another important structural polysaccharide, as it is used by arthropods to build their exoskeleton and in many fungi to build their cell walls.

How does hydrogen bonding allow for the ability to moderate temperature in water?

The ability of water to stabilize temperature steams from its relatively high specific heat (the amount of heat that must be absorbed or released for 1g of that substance to change its temperature by 1°C). This is because heat must be absorbed in order to break hydrogen bonds and released in order to form them; so much heat is needed to disrupt these molecules before water molecules can speed up.

What is a functional group? What are the seven major functional groups?

The chemical groups that affect molecular function by being directly involved in chemical reactions are known as functional groups. 1. Hydroxyl (—OH) 2. Carbonyl (>C=O) 3. Carboxyl (—COOH) 4. Amino (—NH2) 5. Sulfhydryl (—SH) 6. Phosphate (—OP(O3)^2-) 7. Methyl (—CH3) All but the sulfhydryl group are hydrophilic, and all but the methyl group can act as functional groups.

What is dehydration synthesis (polymerization)?

The process by which monomers are linked through covalent bonds with the loss of a water molecule. When a bond forms between two monomers, each monomer contributes part of the water molecule that is released during the reaction: One monomer provides a hydroxyl group (—OH), while the other provides a hydrogen (—H). This reaction is repeated as monomers are added to the chain one by one, making a polymer. (Ex. Protein Synthesis)

What is hydrolysis?

The process by which polymers are disassembled to monomers by essentially reversing the dehydration reaction. Hydrolysis means water breakage, so this implies that the bond between the monomers is broken down by the addition of a water molecule with a hydrogen from water attracting to one monomer and the hydroxyl group attaching the other. (Ex. Digestion)

Why is water considered a polar molecule?

The unequal sharing of electrons and water's V-like shape make it a polar molecule, since it's overall charge is unevenly distributed: the oxygen region of the molecule has a partial negative charge and each hydrogen has a partial positive charge).