AP Biology Unit 2 & Unit 3: Chemistry of Life and Macromolecules

Comprehensive practice flashcards covering AP Biology Unit 2 (The Chemical Context of Life and Water) and Unit 3 (Carbon and the Molecular Diversity of Life), including functional groups, biological macromolecules, chemical bonding, and water chemistry.

What is matter, and what three physical forms can it take in living organisms?

Matter is anything that takes up space and has mass. The vast majority of organisms consist of matter in all three forms: solids, liquids, and gases.

How does an element differ from a compound?

An element is a substance that cannot be broken down into other substances by chemical reactions. A compound is a substance consisting of two or more elements combined in a fixed ratio, exhibiting emergent properties distinct from its individual elements.

What percentage of the $92$ natural elements are essential elements, and what are the top six elements in the human body?

About $20\text{--}25\%$ of natural elements are essential elements. The top six elements in the human body are oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus.

What are the subatomic particles of an atom, where are they located, and what is their approximate mass?

Protons and neutrons reside in the atomic nucleus and each have a mass of approximately $1\,\text{dalton}$ (or atomic mass unit, amu). Electrons form a cloud of negative charge around the nucleus, and their mass is so small it is negligible.

How are atomic number, mass number, and atomic mass defined?

Atomic number is the number of protons in an atom's nucleus. Mass number is the sum of protons plus neutrons in the nucleus. Atomic mass is the total mass of an atom, which can be approximated by its mass number.

What are isotopes, and what are some medical and biological applications of radioactive isotopes?

Isotopes are two atomic forms of an element that differ in their number of neutrons. Radioactive isotopes decay spontaneously, giving off particles and energy; they are applied in dating fossils, X-rays, tracking metabolic pathways, and diagnosing medical disorders such as cancer.

How does electron shell distribution determine an atom's potential energy and maximum electron capacity?

An electron's energy level is correlated with its average distance from the nucleus; potential energy increases with distance. The first shell holds up to $2$ electrons, the second shell holds up to $8$ electrons, and the third shell holds up to $18$ electrons.

What determines the chemical behavior and reactivity of an atom?

The chemical behavior depends mostly on the distribution of valence electrons in the outermost valence shell. Reactivity arises from the presence of one or more unpaired electrons; atoms with completed valence shells obey the octet rule ($8$ electrons) and are unreactive.

What is the difference between nonpolar covalent bonds and polar covalent bonds?

In a nonpolar covalent bond, atoms share electrons equally because their electronegativities are similar. In a polar covalent bond, one atom is significantly more electronegative, pulling the shared electrons closer and creating partial positive ($\delta^+$) and partial negative ($\delta^-$) charges.

How do ionic bonds form, and how are the participating ions defined?

Ionic bonds form via the transfer of valence electrons, resulting in an attraction between oppositely charged ions. A cation is an atom that loses electrons to become positively charged, while an anion is an atom that gains electrons to become negatively charged.

How does a hydrogen bond differ from Van der Waals interactions?

A hydrogen bond forms when a hydrogen atom covalently bonded to an electronegative atom (usually oxygen or nitrogen) is attracted to another nearby electronegative atom. Van der Waals interactions occur when random, asymmetrical electron movements create transient regions of positive and negative charge that weakly attract molecules in close proximity.

Why is molecular shape crucial in biological systems, as exemplified by caffeine and adenosine?

Molecular shape determines how biological molecules recognize and respond to one another. Caffeine has a molecular shape complementary to adenosine receptors, allowing caffeine to bind to the receptors and block adenosine, which normally induces fatigue.

What occurs at chemical equilibrium in a reversible reaction?

Chemical equilibrium is reached when the forward reaction rate and the reverse reaction rate are equal, meaning the relative concentrations of reactants and products remain constant.

What are the four emergent properties of water that facilitate life on Earth?

The four emergent properties are cohesive behavior, high heat capacity, expansion upon freezing, and versatility as a solvent.

How do cohesion, adhesion, and surface tension function in water?

Cohesion is the attraction between water molecules due to multiple hydrogen bonds. Adhesion is the attraction of water to other substances. Surface tension measures how difficult it is to stretch or break the liquid surface, which is unusually high in water due to collective hydrogen bonding.

Why does water possess a high specific heat and high heat capacity?

Water has a high specific heat because heat must first be absorbed to break hydrogen bonds before molecular motion can increase; conversely, heat is released when hydrogen bonds form, allowing water to absorb or release large amounts of heat with minimal temperature change.

How are a calorie and a joule defined, and what is their conversion factor?

A calorie (cal) is the heat required to raise the temperature of $1\,\text{g}$ of water by $1^\circ\text{C}$. A joule (J) is a unit of energy where $1\,\text{J} = 0.239\,\text{cal}$ and $1\,\text{cal} = 4.184\,\text{J}$. One kilocalorie (kcal) equals $1000\,\text{cal}$.

At what temperature does water reach its greatest density, and why does ice float?

Water reaches its greatest density at $4^\circ\text{C}$. As water freezes, its molecules spread out into a rigid crystalline lattice held by stable hydrogen bonds, expanding its volume and making solid ice less dense than liquid water.

How does water function as a versatile solvent, and what are hydration shells?

Because water is polar, it readily dissolves ionic compounds and polar nonionic molecules by forming a hydration shell—a sphere of water molecules surrounding each solute ion or polar region. Nonpolar substances (such as lipids) lack charges and are hydrophobic.

What occurs during the dissociation of water molecules?

A hydrogen ion ($H^+$) is transferred from one water molecule to another, leaving behind a hydroxide ion ($OH^-$) and forming a hydronium ion ($H_3O^+$). By convention, $H^+$ is used to represent the hydronium ion.

How is pH mathematically defined, and what is the ion product of water at $25^\circ\text{C}$?

In any aqueous solution at $25^\circ\text{C}$, the product of hydrogen and hydroxide ions is constant: $[H^+][OH^-] = 10^{-14}$. pH is calculated as $\text{pH} = -\log([H^+])$. Each whole unit change on the scale represents a $10\times$ change in hydrogen ion concentration.

What are typical pH values for human stomach acid and human blood?

Human stomach acid has a pH of approximately $1.5$, whereas human blood has a strictly maintained pH of approximately $7.4$.

Based on this chemical diagram, how does the carbonic acid buffer system stabilize pH in response to a rise or drop in pH?

When pH rises, carbonic acid ($H_2CO_3$) acts as an $H^+$ donor (acid) and dissociates into bicarbonate ($HCO_3^-$) and $H^+$. When pH drops, bicarbonate ($HCO_3^-$) acts as an $H^+$ acceptor (base) and combines with excess $H^+$ to form $H_2CO_3$.

According to the provided diagram on ocean acidification, how does rising atmospheric $CO_2$ inhibit calcification in marine organisms?

Dissolved $CO_2$ reacts with $H_2O$ to form $H_2CO_3$, which dissociates into $H^+$ and $HCO_3^-$. The excess $H^+$ combines with carbonate ions ($CO_3^{2-}$) to form more $HCO_3^-$, reducing the $CO_3^{2-}$ available to react with $Ca^{2+}$ to form calcium carbonate ($CaCO_3$). Carbonate concentrations are predicted to decline by $40\%$ by $2100$.

Why is carbon uniquely suited to serve as the structural backbone of organic macromolecules?

Carbon has four valence electrons, enabling it to form four covalent bonds with a variety of atoms. This tetravalence allows it to form large, complex, and varied molecular chains, branched frameworks, and rings.

What are the four primary ways in which carbon skeletons can vary?

Carbon skeletons can vary in length, branching (unbranched vs. branched), double bond position, and the presence or formation of rings.

Identify the three classes of isomers shown in this diagram and describe how each differs structurally.

Section (a) shows structural isomers, which differ in covalent partners (e.g., pentane and 2-methyl butane). Section (b) shows cis-trans isomers, which differ in spatial arrangement around an inflexible double bond. Section (c) shows enantiomers, which are non-superimposable mirror images around an asymmetric carbon designated as L and D (levo and dextro).

What are the seven functional groups most important to biological chemistry, and what compound classes do they form?

1. Hydroxyl ($-OH$, alcohols); 2. Carbonyl ($>C=O$, ketones and aldehydes); 3. Carboxyl ($-COOH$, carboxylic acids); 4. Amino ($-NH_2$, amines); 5. Sulfhydryl ($-SH$, thiols); 6. Phosphate ($-OPO_3^{2-}$, organic phosphates); 7. Methyl ($-CH_3$, methylated compounds).

What is adenosine triphosphate (ATP), and how does it release energy?

ATP consists of the organic molecule adenosine attached to a string of three phosphate groups. It stores the potential to react with water through hydrolysis, releasing energy that powers cellular processes.

How do dehydration reactions and hydrolysis reactions differ in polymer assembly and breakdown?

In a dehydration reaction, two monomers bond covalently through the loss of a water molecule ($-H$ from one and $-OH$ from the other). In hydrolysis, polymers are disassembled into monomers by adding a water molecule to break the covalent bond.

What sugar molecule is shown in this diagram, what is its chemical formula, and where is it found?

The molecule is ribose, a five-carbon pentose sugar with the molecular formula $C_5H_{10}O_5$, which serves as a vital structural component of RNA.

What type of covalent bond joins two monosaccharides into a disaccharide?

A glycosidic linkage, which is formed through a dehydration reaction that removes a water molecule when joining two hydroxyl groups.

Based on this figure, what are the structural differences among starch, glycogen, and cellulose?

Starch consists of unbranched amylose and somewhat branched amylopectin granules stored in plant plastids. Glycogen is extensively branched and stored in animal muscle and liver tissues. Cellulose is composed of straight, unbranched molecules held together by hydrogen bonds in parallel bundles called microfibrils (bundles of about $80$ cellulose molecules) in plant cell walls.

Why can animals digest starch but not cellulose?

Starch possesses alpha ($\alpha$) glycosidic linkages forming helical polymers, which animal enzymes can hydrolyze. Cellulose possesses beta ($\beta$) glycosidic linkages forming straight polymers; animals lack enzymes to hydrolyze beta linkages, so cellulose passes through as insoluble fiber unless digested by symbiotic microbes.

What is chitin, and where is it naturally found?

Chitin is a structural polysaccharide found in the exoskeletons of arthropods and used to provide structural support to the cell walls of many fungi.

What general property characterizes all lipids, and what enzyme deficiency causes Tay-Sachs disease?

Lipids do not form true polymers and are hydrophobic due to nonpolar hydrocarbon covalent bonds. In Tay-Sachs disease, the body fails to produce functional enzymes needed to break down specific lipids, causing toxic lipid accumulation that impairs motor skills and neural function.

How is a triacylglycerol (fat molecule) constructed, and what linkage joins its subunits?

A triacylglycerol consists of one glycerol molecule (a three-carbon alcohol) joined to three fatty acid tails via ester linkages formed during dehydration reactions.

How do saturated and unsaturated fatty acids differ in structure and physical state at room temperature?

Saturated fatty acids have no double bonds, contain the maximum number of hydrogen atoms, pack tightly, and are solid at room temperature (e.g., butter). Unsaturated fatty acids contain one or more double bonds that cause kinks in the chain, preventing close packing and remaining liquid at room temperature (e.g., olive oil).

Why do phospholipids self-assemble into a bilayer in aqueous environments?

Phospholipids have a hydrophilic head (glycerol attached to a negatively charged phosphate group) and two hydrophobic fatty acid tails; in water, they self-assemble into a bilayer with hydrophobic tails sequestered inside and hydrophilic heads facing the aqueous exterior.

What is the structural characteristic of steroids, and what role does cholesterol play?

Steroids are lipids characterized by a carbon skeleton composed of four fused rings. Cholesterol is an essential steroid embedded in animal cell membranes, though elevated blood concentrations contribute to atherosclerosis.

What are the five structural parts of an amino acid monomer?

Each amino acid contains: 1. A central carbon atom (alpha carbon); 2. A hydrogen atom; 3. A carboxyl group ($-COOH$); 4. An amino group ($-NH_2$); 5. A variable side chain (R group) that determines the amino acid's identity.

According to the provided amino acid classification chart, what are the three major chemical categories of side chains (R groups)?

The three categories are: nonpolar side chains (hydrophobic, e.g., Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro); polar side chains (hydrophilic, e.g., Ser, Thr, Cys, Tyr, Asn, Gln); and electrically charged side chains (hydrophilic, split into acidic negatively charged Asp and Glu, and basic positively charged Lys, Arg, and His).

What biochemical reaction and structural features of polypeptide formation are illustrated in this diagram?

The diagram illustrates the formation of a peptide bond through a dehydration reaction between the carboxyl group of one amino acid and the amino group of an incoming amino acid. The resulting chain features a repeating backbone, variable R groups, an amino end (N-terminus), and a carboxyl end (C-terminus).

What are the four levels of protein structure, and which bonds or interactions stabilize each level?

Primary: unique linear sequence of amino acids (peptide bonds). Secondary: localized coiling or folding (alpha helices and beta pleated sheets) stabilized by hydrogen bonds between backbone constituents. Tertiary: overall 3D shape resulting from R-group interactions (hydrogen, ionic, hydrophobic interactions, and disulfide bridges). Quaternary: association of two or more polypeptide subunits.

What protein visualization models and simplified representations are shown in this diagram?

The top row shows the space-filling model, ribbon model, and wireframe model (with a bound yellow target molecule). The bottom row shows a transparent shape outlining rhodopsin contours, a solid shape for generic structures, a simplified enzyme shape, and a single dot representing a secreted protein such as insulin.

Why can primary protein structure not be denatured?

Denaturation disrupts weak interactions (hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bridges) that hold secondary, tertiary, and quaternary structures together, but it does not break the covalent peptide bonds defining the primary sequence.

What is the molecular cause and physiological consequence of sickle cell disease?

Sickle cell disease is caused by a single amino acid substitution in the protein hemoglobin, which changes the shape of red blood cells into sickled forms that clog small blood vessels, leading to painful sickle cell crises.

How do purines and pyrimidines differ in structure, and which bases belong to each family?

Pyrimidines have a single six-membered ring and include cytosine (C), thymine (T, in DNA only), and uracil (U, in RNA only). Purines have a double-ring structure (a six-membered ring fused to a five-membered ring) and include adenine (A) and guanine (G).

How does nucleotide structure determine the antiparallel directionality of a DNA double helix?

Each nucleotide has a phosphate group attached to the 5' carbon and a hydroxyl group on the 3' carbon of pentose sugar. In a DNA strand, adjacent nucleotides link via phosphodiester bonds, giving the strand a 5' to 3' orientation; in the double helix, the two complementary strands run in opposite directions (antiparallel).

What base-pairing rules govern DNA, and how many hydrogen bonds stabilize each pair?

Adenine (A) pairs specifically with thymine (T) via $2$ hydrogen bonds, while guanine (G) pairs with cytosine (C) via $3$ hydrogen bonds. Each pair combines a purine with a pyrimidine to maintain consistent double helix width.

According to the provided cell diagram, what three major steps constitute gene expression?

Step 1: Synthesis of mRNA from DNA within the nucleus. Step 2: Movement of mRNA out of the nucleus into the cytoplasm. Step 3: Synthesis of a polypeptide protein on a ribosome using the genetic sequence carried by the mRNA.

What are bioinformatics, genomics, and proteomics?

Bioinformatics is the use of computer software and computational tools to process and analyze biological sequence data. Genomics is the approach used to analyze large sets of genes or compare entire genomes between species. Proteomics is the large-scale analysis of whole protein sets and their properties.