AP Biology Exam Prep Flashcards***mostly from units 1-3 +Cell signaling

Living things use the energy in organic molecules to power their metabolisms. This occurs differently, depending on whether or not oxygen is present. 1) List the four phases of energy harvest that occur when oxygen is present. 2) Describe the location of each phase, and its primary products. 3) Contrast that with what happens when oxygen isn't present.

1 and 2) When oxygen is present, organic molecules will be processed through the enzyme catalyzed reactions of aerobic cellular respiration. This begins with glycolysis, which takes glucose and uses its chemical energy to generate ATP and NADH. This occurs in the cytoplasm, and ends with the production of the 3 carbon molecule pyruvic acid. Next is the link reaction, which brings pyruvic acid into the mitochondria and converts it into Acetyl CoA, generating NADH. This is followed by the Krebs cycle, which occurs in the mitochondrial matrix. These reactions oxidize Acetyl CoA, using the energy released to produce NADH and ATP. Cellular respiration ends with the electron transport chain (ETC), which occurs along the inner mitochondrial membrane. The ETC oxidizes NADH and FADH2, using the resulting electron flow to power creation of ATP. 3) If oxygen is not present, organic molecules like glucose will anaerobically fermented, producing a small amount of ATP. This occurs in the cytoplasm.

List three phenomena that involve hydrogen bonding. Limit your response to processes that directly involve water molecules.

1) Because of water's polar covalent structure, adjacent water molecules form hydrogen bonds with one another. This allows any body of water to absorb a lot of heat energy before its temperature increases. That's because the hydrogen bonds constrain the movement of the water molecules in that body, and temperature is average kinetic energy of the molecules within an object. Because of hydrogen bonding, the water molecules resist increased movement. One such watery body that resists wide temperature fluctuations is your body (or the body of any relatively large animal). Hydrogen bonds help keep the temperature within your body relatively constant. 2) On a larger scale, hydrogen bonds allow large bodies of water to absorb lots of heat energy as the temperature of the environment increases. That helps to create moderate temperatures in any region near a large body of water (a large lake or an ocean). This also has a moderating effect on the climate of the Earth as a whole (since 3/4 of Earth's surface is covered by oceans), keeping our planet's temperature optimal for life. 3) Because the breaking of hydrogen bonds requires energy, water has a very high heat of vaporization. That means that when water is converted into water vapor (which happens when sweat evaporates from human skin or from a dog's tongue), it carries away a lot of heat energy, lowering the temperature of the body that it evaporated from. This is how evaporative cooling works, and it's a key thermoregulatory adaptation in humans and other animals.

1) Describe the structure and function of chloroplasts. 2) Describe the evolutionary origins of chloroplasts, and provide evidence.

1) Chloroplasts, like mitochondria, are double-membraned organelles. Like mitochondria, they contain their own DNA and ribosomes, and replicate themselves through binary fission. Chloroplasts have internal membrane-bound sacs called thylakoids which contain the membrane-bound photosystems and chlorophyll pigments for the light reactions of photosynthesis. The thylakoids are organized into stacks called grana. Surrounding the grana is a fluid called stroma, which is where the carbon-fixing reactions of the Calvin cycle occur. 2) The double membrane of chloroplasts, along with their DNA, ribosomes, and reproduction through binary fission, is evidence for the origin of chloroplasts as independent cyanobacteria that were taken up by an early eukaryotic cell. This cyanobacterium evolved into the chloroplast. The result of this endosymbiotic merger led to algae and plants.

1) Describe the endoplasmic reticulum. 2) List the two forms of endoplasmic reticulum, and describe their structural and functional differences.

1. The endoplasmic reticulum is an interconnected series of channels found between the nuclear membrane and Golgi body in eukaryotic cells. 2. There are two forms of E.R., rough and smooth. Rough ER is studded with ribosomes. Proteins that are destined for inclusion in a lysosome, in any other organelle, in the cell membrane, or for export from the cell are synthesized at the rough E.R. The smooth ER lacks ribosomes. It's usually on the outer side of the ER network. While it lacks ribosomes, it has many embedded enzymes. These enzymes vary in function depending on the tissue in which the cell is found. In some endocrine glands, the smooth ER produces steroid hormones from cholesterol. In the liver, the smooth ER's enzymes convert various toxins into a soluble form, enabling them to be excreted from the body. Another smooth ER enzyme in the liver is glucose-6-phosphate, which plays a key role in converting glycogen into glucose.

1) What are neurotransmitters? 2) Explain how neurons use neurotransmitters to signal their postsynaptic targets.

A neurotransmitter is a substance that's released at the end of a neuron's axon. By diffusing across a synapse (the tiny space between a neuron and its target) the neurotransmitter can relay an impulse to a postsynaptic neuron, a muscle, a gland, etc. 2) Here are the details. When an action potential arrives at the end of an axon, it causes a change in voltage-gated calcium channels, causing these channels to open and allowing calcium ions to diffuse from the extracellular fluid outside the membrane of the axonal bulb into the axon itself. Once in the axonal bulb, the calcium ions induce cytoplasmic changes that, in turn, induce exocytosis in vesicles storing neurotransmitter. This releases neurotransmitter into the synapse. The neurotransmitter then diffuses across the synapse, binding with receptors on postsynaptic dendrites (or on other targets, such as muscle cells or glands). These receptors are connected to ligand-gated channels, and the effect of the neurotransmitter binding with these receptors depends on the neurotransmitter and the properties of the channel. If binding opens sodium channels, which allow sodium ions to diffuse into the postsynaptic cell, the result is excitation of the postsynaptic cell, increasing the chance that it will respond. If binding opens potassium channels, then potassium ions will diffuse out of the postsynaptic cell, resulting in inhibition of the postsynaptic cell (decreasing that chance that it will respond).

In terms of hydrogen ions, hydroxide ions, and pH, describe the difference between an acidic and a basic solution.

Acidic solutions have more hydrogen ions (protons or H+) than hydroxide ions (represented by OH-) The pH of an acidic solution is below 7. Bases are substances that have more hydroxide ions than hydrogen ions, and their pH is above 7.

Explain how molecular directionality works in proteins, and why this is biologically significant.

Amino acids are built around a central carbon. On one side is an amino group, and on the other side is a carboxyl group. Peptide bonds are formed between amino acids when ribosomes, during protein synthesis, form a covalent bond between the amino group of one amino acid and the carboxyl group of the next. One consequence of this is that every protein has an amino group on one end, and a carboxyl group on the other end. The part of the chain that ends with an amino acid is called the amino terminus. The other side is the carboxyl terminus. This is biologically significant during both protein synthesis and protein digestion. During synthesis, ribosomes can only add new amino acids at the carboxyl terminus of a polypeptide chain. During protein digestion, protein digesting enzymes, which can be intracellular or in body compartments (like the stomach) will have active sites that can pull proteins apart in specific ways. Some will break off amino acids from the amino side (but be unable to do so from the carboxyl side). Others attack the carboxyl end. Others can hydrolyse peptide bonds in the middle of a polypeptide chain.

Describe the consequences of being in a hypotonic or hypertonic environment for animal and plant cells.

An animal cell in a hypotonic environment will take up water as water flows from the hypotonic environment into the cell. The cell will expand, and eventually burst. In a hypertonic environment, an animal cell will shrink and shrivel as it loses water. A plant cell in a hypotonic environment will take up water as water flows into the cell. The cell will expand, but its expansion will be limited by the cell's rigid cell wall. The cell will become turgid, which is a healthy condition for a plant cell. In a hypertonic environment, water will flow out of a plant cell. This will pull the membrane away from the cell wall. The lack of pressure will cause the plant itself to wilt.

Explain how the central vacuole in a plant cell responds to changes in a plant's environment.

As water moves into a plant, following a water potential gradient, water will enter cells and move into a plant cell's central vacuole. As the vacuole fills with water it expands, pushing against the plant cell wall. This outward pressure is called turgor, and it keeps plants full and firm (imagine a crispy lettuce leaf). If plants are low on water, the force of turgor diminishes, and plants wilt in response.

Describe how steroid hormones (such as testosterone or estrogen) work.

Because they're non-polar, steroid hormones are able to diffuse through the phospholipid bilayer portion of the membrane. In other words, unlike their protein counterparts, steroid hormones don't have to bind with membrane receptors and activate second messengers, but rather diffuse right into the cytoplasm. Once they pass through the membrane, steroid hormones bind with mobile cytoplasmic receptors that are floating in the cytoplasm. Binding with these mobile receptors creates a hormone-receptor complex, which can diffuse through nuclear pores and enter the nucleus. Once in the nucleus, the hormone-receptor complex acts as a transcription factor, binding with specific DNA sequences and activating genes. "Activating genes" means allowing RNA polymerase to bind with a gene's promoter, resulting in transcription into RNA. Once processed, the RNA enters the cytoplasm as mRNA, where it is translated into protein. This often causes long-term cellular changes: imagine the changes associated with puberty, which are caused by steroid hormones such as testosterone and estrogen. Again, this is in distinction to protein hormones, which act through second messengers and signal transduction cascades, causing very quick changes that can also be very quickly deactivated.

What happens between glycolysis and the Krebs cycle?

Between glycolysis and the Krebs cycle is the Link reaction. After glycolysis, pyruvic acid is transported across the outer and inner mitochondrial membranes into the mitochondrial matrix. In the matrix, an enzyme decarboxylates pyruvate, releasing carbon dioxide (accounting for 1/3 of the carbon dioxide released during cellular respiration). Other enzymes oxidize the resulting two carbon molecule, powering reduction of NAD+ to NADH (the energy of which will later be harvested in the electron transport chain). The two-carbon acetyl group that results is attached to coenzyme A, generating Acetyl-CoA, the starting point for the Krebs cycle.

Compare and contrast ATP generation in mitochondria and chloroplasts.

Both mitochondria and chloroplasts generate ATP through the same chemiosmotic mechanism. Both processes use the energy of flowing electrons to power proton pumps that pump protons into an enclosed compartment. The only way for protons to diffuse out of this chamber is through the channel and enzyme ATP synthase, which uses the energy of these diffusing protons to power the formation of ATP from ADP and inorganic phosphate. In the mitochondria, the flow of electrons is powered by energy from food. The electrons flow along the electron transport chain in the inner mitochondrial membrane, and proton pumps use the energy from these electrons to pump protons from the matrix to the intermembrane space. Protons subsequently diffuse through ATP synthase from the intermembrane space back to the matrix. In chloroplasts, the electron transport chain is located in the thylakoid membrane. The source of electrons is water, and the flow of electrons powers proton pumps that pump protons from the stroma into the thylakoid space. The subsequent diffusion of protons from the thylakoid space back to the stroma, via the ATP synthase channel, is what powers synthesis of ATP from ADP and inorganic phosphate.

Starch and cellulose are both polysaccharides, yet their biological functions are different. Describe the function of each, and explain their differences.

Both starch and cellulose are polymers. Starch is used by plants to store energy; cellulose is used to build cell walls. Starch can be used for energy storage because the bond that connects the glucose monomers in starch is one that's easily hydrolyzed by enzymes in many species, including humans. Cellulose, by contrast, can't be digested by humans. That's because the bonds between the glucose monomers in cellulose have a configuration that few animal enzymes can hydrolyze. As a result, cellulose, when ingested, serves as a source of fiber, but not of energy. However, some animals have formed symbiotic mutualistic relationships with microorganisms that enable them to break down cellulose in a way that releases its energy. Among the mammals, ruminants have symbiotic relationships with bacteria that can break off the glucose monomers in cellulose. As a result, ruminants can digest grass and other fibrous plants, and use these foods for energy. Termites have a symbiotic relationship with a protist (a single celled eukaryote, which carries its own bacterial endosymbiont). This enables termites to use wood as a food from which they can derive energy.

Describe the basic structure and biological importance of carbohydrates.

Carbohydrates consist of monosaccharides, disaccharides, and polysaccharides. Monosaccharides such as glucose are often energy sources, powering cellular respiration. Glucose is also the product of photosynthesis, so it's the way that carbon, the central atom in living things, enters the biosphere. Disaccharides like lactose and sucrose are often used for energy transfer (lactose transfers energy from a mammalian mother to her offspring; sucrose transfers energy from the leaves of a plant to other, non-photosynthetic parts). Polysaccharides like starch and glycogen are used for energy storage (starch in plants, glycogen in animals), while cellulose is used to build the cell walls of plants.

What are the four types of macromolecules that make up living organisms.

Carbohydrates, lipids, proteins, and nucleic acids.

Describe the biological importance of carbon, and explain why carbon plays the role that it does in living things.

Carbon is the central atom in biological molecules. It's central to the structure of carbohydrates, lipids, proteins and nucleic acids. Carbon's central role stems from its atomic structure: it has six protons, along with six neutrons and six electrons. The six electrons are organized so that carbon has four valence electrons, allowing carbon to form a wide variety of covalent bonds, including single, double, and triple bonds with itself and other elements. Because carbon can bond with itself, and form double and triple bonds, it can form rings, chains, and branched molecules that are indeterminate in length and shape. This is a capability that no other element (not even silicon) has, and it made possible the evolution of complex molecules that, at a molecular level, underlie life's properties: replication, energy transfer, encapsulation, etc.

Describe the fluid mosaic model of cell membranes.

Cell membranes can be described as fluid mosaics. They're fluid because their components are in constant motion, moving laterally within the plane of the membrane. They're mosaics because they're composed of a variety of pieces: phospholipids, proteins, and additional molecules like cholesterol. On the membrane's inside and outside, various additional molecules might be attached to proteins or phospholipids, including glycoproteins and glycolipids.

List the three overall processes by which membranes control a cell's internal environment.

Cell membranes control the cell's internal environment through three overall processes: 1) by selectively controlling what molecules can diffuse into and out of cells, 2) through pumping molecules in or out of the cell by active transport, and 3) through bulk transport (endocytosis and exocytosis).

Membranes are fundamental to life. Why?

Cells are highly complex, organized structures. To maintain this organization, cells need to be separated from the environment that's around them, and then work to maintain an internal environment that's different from their external environment. The membrane is the basis of this separation, and many life processes are about moving things across membranes in way that differentiates the internal environment of the cell from its external environment.

On the most fundamental level, what are the two ways that cells communicate with one another?

Cells can communicate with one another by direct contact, or by sending chemical signals to one another. These chemical signals might travel very short distances between cells that might be close to one another (as in paracrine signaling), or between distant parts of the body (endocrine signaling), or between different organisms (pheromone signaling).

Describe some examples where individual cells or entire organisms need to increase their surface area. Describe how they do this.

Cells or organisms may need additional surface area in order to increase the amount of molecules that can enter or leave by diffusion, or to increase available surface for radiation of heat from the body to the environment. Cells might also need more working surface for membrane-embedded enzymatic reactions. An example of increasing the surface for diffusion of molecules is seen in structures like root hairs in roots, the gills of fish (which are organized as thin sheets of tissue) or the epithelial cells that make up the lining of the gut (which have a highly folded shape). Structures organized for increasing working surface for enzymatic reactions include the highly folded endoplasmic reticulum or inner mitochondrial membrane. Flattened structures also have lots of surface area relative to their volume: these include structures like the flattened sacs of the Golgi complex or the grana (flattened stacks of thylakoid sacs) in chloroplasts. On a much larger level, the flat ears of elephants, or the dorsal sail of the ancient mammal-like reptile Dimetrodon, are adaptations that increase surface area for radiating heat into the environment.

Cellular compartmentalization marks a major evolutionary advance. Specify when and how that advance occurred, and describe the advantages that compartmentalization provides.

Cellular compartmentalization is the innovation that separates eukaryotic from prokaryotic cells. That means that compartmentalization can be dated back to the origin of eukaryotic cells, which arose about 2 billion years ago. It's widely thought that compartmentalization initially arose through endosymbiosis, specifically by the incorporation of the ancestor of mitochondria (which was a bacterial cell) into an archaeal cell. Cellular compartmentalization is adaptive in several ways. On a big picture level, having multiple ATP-producing mitochondrial endosymbionts within each cell made much more ATP available to the host cell, allowing it to grow in size and complexity. This set the stage for multicellularity. On a more immediate, cellular level, the compartmentalization that followed the incorporation of mitochondria led to the development of the endomembrane system. This allowed for the creation of membrane-enclosed compartments that could have an internal chemistry that differed from the cytoplasm as a whole. For example, the interior of a lysosome contains hydrolytic enzymes that can safely work within the lysosome, without exposing the rest of the cell's volume to these hydrolytic enzymes. Similar regions of unique chemistry can be found in the ER, the Golgi, or vacuoles.

Explain how variation in chlorophyll types increases the efficiency of photosynthesis.

Chlorophyll is the key light absorbing pigment in photosynthesis. Green plants have two main types: chlorophyll a and chlorophyll b. The difference between the two types comes down to a single functional group: chlorophyll a has a methyl group whereas chlorophyll b has an acetyl group. Whereas the peak absorption of chlorophyll a is in the red part of the spectrum, the peak absorption of chlorophyll b is in the blue portion of the spectrum. Having both types of chlorophyll thus increases the amount of light energy that plants can use during photosynthesis. Chlorophyll b is particularly prevalent in shade-adapted plants.

Describe the structure of DNA.

DNA consists of two nucleotide strands. Within each strand, the deoxynucleotide monomers are connected to one another by sugar-phosphate bonds. The strands connect to one another by hydrogen bonds between nitrogenous bases with complementary shapes: adenine bonding with thymine with two hydrogen bonds, and cytosine binding with guanine with 3 hydrogen bonds. The shapes of the nitrogenous bases only complement one another, however, when the nucleotides are oriented upside down relative to one another. Hence, the two strands are antiparallel to one another, with one strand running 5' to 3' in one direction, and its complement running 5' to 3' in the opposite direction.

What is photosynthesis? Describe its evolutionary origins, and its Earth-changing consequences.

During photosynthesis, free energy from light is coupled to synthesis of organic compounds. There are a variety of forms: in the one that happens in plants, algae, and Cyanobacteria, carbon dioxide is combined with water to create carbohydrates, with oxygen released as a byproduct. Photosynthesis evolved relatively early in the history of life — as early as 3.5 billion years ago. There is fossil evidence of microscopic cells that look like modern Cyanobacteria (photosynthetic bacteria), and which have left chemical traces indicating that they were converting carbon dioxide into organic matter. These early photosynthesizers transformed earth by releasing free oxygen (O2) into the environment. The evidence for this is in massive deposits of iron oxide that precipitated out of the oceans, creating banded iron formations that are dated at about 2 billion years ago. The same process led to the formation of Earth's oxygen-rich atmosphere, which led to the ozone layer that made life on land possible (starting at about 400 million years ago). Photosynthetic plants, and the algae that preceded plants, emerged much more recently than these Earth-transforming Cyanobacteria. Algae are eukaryotes, and didn't emerge until about 2 billion years ago, when a eukaryotic, mitochondrion-containing cell took up the ancestor of chloroplasts in the second great instance of endosymbiosis in Earth's history. This led to the green algae. Plants didn't emerge until the ozone layer (described above) made life on land possible, about 400 million years ago.

What happens during the Krebs Cycle?

During the Krebs cycle, energy from food, brought into the cycle in the form of acetyl-CoA, is used to generate ATP from ADP and inorganic phosphate, and to chemically reduce the electron carriers NAD+ and FADH to NADH and FADH2. These electron carriers will later power the electron transport chain's conversion of ADP and inorganic phosphate to ATP through chemiosmosis. Here are some details. Enzymes transfer the two carbon acetyl group from Acetyl-CoA to oxalic acid, a four carbon molecule. This creates citric acid, a six carbon molecule. In subsequent reactions, citric acid is oxidized, and its electrons are used to reduce the electron carriers NAD+ and FADH to NADH and FADH2. Other reactions use the chemical energy in citric acid to power a substrate-level phosphorylation of ADP and inorganic phosphate into ATP. For each acetyl-CoA that enters the cycle, one ATP, one FADH2, and three NADHs are generated. As this occurs, carbon dioxide is released as a waste product (accounting for 2/3 of the CO2 produced during cellular respiration).

What is endosymbiosis? Describe how it happened, along with the evidence for the idea that chloroplasts and mitochondria were once free living bacterial cells that arose through endosymbiosis.

Endosymbiosis means "living together, on the inside." In terms of mitochondria and chloroplasts, it refers to the idea that these organelles were once free-living bacterial cells that took up residence in other cells. The process began with endosymbiosis of the ancestor of mitochondria by an archaeal cell. This event gave rise to all of the eukaryotes. Later a mitochondria-containing eukaryotic cell took up chloroplasts, producing the line of organisms that includes plants and algae. There are at least 3 lines of evidence supporting this idea. - First, both organelles (mitochondria and chloroplasts) have their own DNA, and this DNA is organized into a circular chromosome that is similar to a bacterial chromosome. - Second both organelles use their own ribosomes to produce some of their own proteins. These ribosomes resemble bacterial ribosomes in terms of their rRNA sequence and structure. - Finally, both chloroplasts and mitochondria have double membranes. The outer membrane is thought to be a vestige of the host cell membrane that engulfed the ancestral mitochondrion and chloroplast when the endosymbiotic relationship first arose nearly two billion years ago.

Describe the key properties of enzymes.

Enzymes are large molecules (usually proteins, but sometimes RNAs) that catalyze reactions in cells. They act to lower the activation energy of the reactions that they catalyze, greatly increasing the rate of these reactions. Enzymes are specific, and their specificity derives from the fact that they have an active site that has a shape and charge that complements the shape and charge of their substrate (the substance that an enzyme acts upon).

Unlike inorganic catalysts, enzymes are both highly specific, and tend to have a narrow set of conditions where they can function at or near their optimum. Explain.

Enzymes, with a few important exceptions (like catalytic RNAs) are proteins. Protein shape emerges from interactions between the amino acids making up the protein. These interactions included relatively weak hydrogen bonds, ionic bonds, and hydrophobic clustering. Changes in environmental factors such as pH, temperature, or ion concentration will interfere with these bonds, changing the protein's overall shape. If the shape is changed at the active site, then the enzyme will no longer be able to bind with its substrate. As a result, most enzymes have a pH, ionic, or temperature optimum at which their shape best fits their substrate. Moving away from this optimum causes denaturation: a change in the shape that lowers (or completely negates) the enzyme's function.

Compare and contrast the chemical structure, properties, and functions of of fats and oils.

Fats and oils are both triglycerides. Triglycerides consist of three fatty acids bonded to a glycerol molecule (a 3-carbon alcohol). In fats, the fatty acids are saturated. That means that the hydrocarbon chains in a fat have no double bonds. As a result, the chains are straight, allowing the fat molecules to form weak intermolecular bonds with one another (called "London Dispersion forces). While the bonds are weak, they're sufficient to enable a cluster of fat molecules to maintain their shape at room temperature, which is why fats are solids. In oils, one or more of the fatty acids is unsaturated, meaning that they have at least one double bond. This bends the hydrocarbon chains, which prevents oil molecules from forming the intermolecular bonds found in fats. As a result, oils are liquid at room temperature. Both fats and oils are used for energy storage. In animals, fats also serve as insulation.

Compare and contrast fats and oils.

Fats and oils both have the same overall molecular structure: three fatty acids bonded to a 3-carbon alcohol called glycerol. The difference is that in fats, the fatty acids are saturated. All of the carbons in the hydrocarbon chains of the fatty acids are single bonded to one another, with the rest of their bonds filled with single bonds to hydrogen atoms. This saturation makes the hydrocarbons straight, and multiple fat triglycerides will form weak bonds with one another by London dispersion forces, enabling fats to be solid at room temperature. Unsaturated fats have one or more double bonds between the carbon atoms in their fatty acid chains. These double bonds cause the fatty acid chains to bend. These bends create distance between the oil triglycerides, keeping them from forming intermolecular bonds. As a result, oil is liquid at room temperature.

What happens during glycolysis? Include cellular locations, inputs, and outputs in your answer.

Glycolysis occurs in the cytoplasm. Its starting substrate is glucose. In a series of enzyme catalyzed reactions, glucose is phosphorylated (investment phase), then split into two molecules of G3P (cleavage phase). Then G3P is oxidized, which provides the electrons needed to reduce the electron carrier NAD+ to NADH. Other enzymes use the chemical energy in G3P to power a substrate level phosphorylation that generates two ATPs from ADP and organic phosphate. The net yield of glycolysis is 2 ATPs and 2 NADH. The series of reactions ends with two molecules of the 3-carbon molecule pyruvate (also known as pyruvic acid).

Explain how variation in hemoglobin maximizes oxygen absorption in humans and other placental mammals at various life stages.

Hemoglobin is the protein that transports oxygen in red blood cells in almost all vertebrates. Before birth, humans and other mammals produce fetal hemoglobin, a hemoglobin variant that has a much higher affinity for oxygen than adult hemoglobin. Because of that, oxygen will diffuse from the mother's red blood cells to those of the fetus. Within about six months after birth, production of fetal hemoglobin is replaced by production of adult hemoglobin.

Explain the molecular cause and overall biology of sickle cell disease.

Hemoglobin is the protein that transports oxygen in red blood cells. It's a globular protein that consists of four polypeptide chains. Two of these are identical alpha chains, and two are identical beta chains. The beta chain consists of 146 amino acids. People suffering from sickle cell disease are homozygous for a recessive mutation in which the DNA that codes for the beta chain substitutes the amino acid valine (which has a nonpolar side chain) for glutamic acid (which has an acidic side chain). This changes the overall chemistry of the resulting hemoglobin protein in such a way so that when blood becomes deoxygenated (something that happens to blood all of the time as blood delivers up oxygen to the cells), the mutated hemoglobin molecules form hydrophobic bonds with one another, causing them to aggregate into fibers. This reduces the capacity of hemoglobin to carry oxygen, and deforms the shape of red blood cells. Instead of smooth, indented disks, the cells become elongated and spiked. This in turn, causes these cells to become trapped in capillaries (the smallest blood vessels). This impedes blood flow, causing pain and tissue damage. Heterozygotes, with only one mutated version of the hemoglobin gene, can experience a small amount of sickling, but not enough to generate the pain crises and tissue damage experienced by homozygotes. However, the change in hemoglobin chemistry creates a hostile environment for the Plasmodium parasite that causes malaria. The result is that heterozygotes have resistance to malaria, increasing the frequency of the sickling allele in populations that live in malaria-prone areas. This phenomenon is called "heterozygote advantage," and it can explain the high frequency of an allele that is harmful in homozygotes.

Explain the biological importance of hydrogen.

Hydrogen is a key atom in every biological molecule. As an ion, hydrogen also plays a key role in life's most basic energy process, chemiosmosis, during which hydrogen ions (H+) get pumped into some sequestered space (such as the mitochondrial intermembrane space, or the thylakoid space), storing up energy that's used in the synthesis of ATP as these hydrogen ions diffuse through the ATP synthase channel. This flow of hydrogen ions is central to both cellular respiration (in the mitochondria), and photosynthesis, which can be thought of as a way by which carbon dioxide is hydrogenated to create glucose and other carbohydrates.

Compare and contrast the terms hypotonic, hypertonic, and isotonic, and use these terms to explain the flow of water into or out of cells.

Hypotonic, hypertonic, and isotonic are all relative terms. If a cell is in a hypotonic environment, that means that the solution that the cell is in has less solute and more water than does the cell under consideration. Because water always flows from hypotonic (where the water is more concentrated) to hypertonic, water will flow from the hypotonic solution into the cell. The cell, in short, will gain water. A cell in a hypertonic environment is in the reverse situation. In this case, the cell's environment has relatively less water and more solute than the cell does. This makes the cell hypotonic to its environment, and water will flow from the cell to its environment. The cell will lose water. A cell in an isotonic solution has the same concentration of solutes and water as the solution that its in. Water will flow into and out of the cell at the same rate, so it neither gains or loses water.

What happens after glycolysis if oxygen is not present?

If oxygen is not present, the pyruvic acid generated during glycolysis is fermented. Fermentation involves chemically reducing pyruvate by oxidizing NADH (a key product of glycolysis) back to NAD+. Why? Because the two ATPs generated by glycolysis are better than none. NAD+ is a required substrate for glycolysis, and its regeneration enables glycolysis to continue to create ATP (even in the absence of oxygen). Reduction of pyruvate can result in a variety of products. In lactic acid fermentation, lactic acid (a 3-carbon molecule) is produced. In alcohol fermentation, pyruvate is decarboxylated (loses a carboxyl group) and reduced, producing ethanol (the two-carbon alcohol in wine, beer, and spirits) and carbon dioxide.

In a controlled experiment, 1) why do you need a control group, and 2) what's the difference between the control group and the experimental group?

In a controlled experiment, 1) why do you need a control group, and 2) what's the difference between the control group and the experimental group? In a controlled experiment, the experimental group is the group that gets exposed to the independent variable (the thing that you're testing). The control group is identical to the experimental group in every possible way, except for that the subjects in the control group are not exposed to the independent variable. That makes the control group a standard of comparison: it lets you see the effect of the independent variable, because any difference between the two groups should be attributable to the independent variable.

In a controlled experiment, what's the difference between the independent and dependent variable? Provide an example.

In a controlled experiment, the independent variable is the thing that you're testing. It's the thing to which you expose the subjects in your experimental group (as opposed to the subjects in your control group, which don't get exposed to the independent variable). The dependent variable is the measured outcome. If the independent variable has an effect, you should be able to measure that effect as a difference between what happens in your experimental group and your control group. Example 1: If you were designing an experiment to see the effect of light wavelength on the rate of photosynthesis, then your independent variable could be the wavelength of the light, and the dependent variable could be oxygen produced, or carbon dioxide consumed, or rate of growth, etc. in an population of plants growing under controlled conditions. Example 2: If you were designing an experiment to test the effect of temperature on respiration, then your independent variable could be the temperature, while the dependent variable could be the rate of oxygen consumption, or the rate of carbon dioxide production, in a population of respiring beans in a respirometer.

Compare and contrast competitive and noncompetitive inhibition.

In competitive inhibition, a molecule that's not the enzyme's substrate blocks the enzyme's active site. In order for this to happen, the competitive inhibitor must have, in part of its structure, a shape that's similar to the shape of the enzyme's substrate. This keeps the substrate from binding, inhibiting the rate of the reaction. In non-competitive inhibition, a molecule binds away from the active site, at a region called the allosteric site. Binding at the allosteric site has a ripple effect throughout the protein, causing a change in the shape of the active site which diminishes or blocks enzyme activity.

Compare compartmentalization in prokaryotic and eukaryotic cells

In general, prokaryotic cells are not compartmentalized, though they do have internal regions with specialized structures and functions. Eukaryotic cells are highly compartmentalized, with many internal membranes that divide the cell into regions with distinct structures, chemistry, and functions. Examples of cellular compartments within eukaryotic cells include lysosomes, the E.R., the Golgi complex, and vacuoles.

Explain how humans and other mammals use ADH for osmoregulation.

In humans and other mammals, blood osmolarity is monitored by the brain's hypothalamus. When blood osmolarity increases beyond the set point (meaning that your body needs more water), your hypothalamus signals the pituitary gland to release ADH, antidiuretic hormone. ADH has two targets: one is activating nerve pathways that encourage you to drink water. Drinking water decreases the blood's osmolarity as more solvent gets added to your blood. Simply put, ADH makes you feel thirsty, and drinking restores homeostasis. Until you can take a drink, ADH also acts on the collecting ducts of the kidneys. The collecting ducts are tubes that contain a fluid that you can think of as "pre-urine." This "pre-urine" contains toxins that have been filtered out of the blood. Its next stop is the ureters, tubes that bring urine to the bladder, after which you'll urinate this fluid out of your body. ADH acts on the collecting duct in a way that increases the number of aquaporins in the cells of the duct. This increases the amount of water that can diffuse out of this pre-urine. Your urine becomes more concentrated (darker), and the water that's been pulled out can diffuse back into your blood. This keeps solvent in your blood, keeping the osmolarity of the blood from rising further (until you can get that drink of water).

Explain how variation in phospholipid structure can serve an adaptive function in browsing mammals that forage in snowy environments.

In mammals such as elk that walk through the snow as they forage for food in winter, there's typically a gradient of phospholipid structure in the membranes of the cells in their legs: closer to the hoof, the cell membranes tend to have phospholipids with more unsaturated fatty acid tails. Closer to the body core, the phospholipids tend to have more saturated fatty acid tails. This is an adaptation to maintain membrane fluidity at the right level, despite the differences in temperature experienced by these cells. Even though, as a mammal, the elk maintain their overall internal body temperature, the temperature in their extremities is allowed to drop far below the temperature in the core (just as your hands and feet are often much colder than the temperature of your trunk and head). Having more unsaturated fatty acids in the phospholipids of the membranes toward the hoof keeps those membranes fluid. By contrast, closer to the core the phospholipids have more saturated fatty acids, which also maintains the right amount of membrane fluidity in those cells. Membrane fluidity, in turn, establishes conditions for proper diffusion of substances across the membrane.

What is positive feedback? Describe how positive feedback functions during childbirth and fruit ripening.

In positive feedback, a stimulus feeds back to a system in a way that increases the activity of the system. During childbirth, the baby's head pushes against its mother's cervix (the tip of the uterus at the end of a female mammal's vagina). This causes the tissue in the cervix to stretch. Nerve impulses from the cervix to the brain cause the release of a hormone called oxytocin from the pituitary gland. Oxytocin diffuses throughout the bloodstream: when it arrives at the uterus, it causes the cervix and uterine muscles to contract. This increases the pushing of the baby's head against the cervix, which feeds back to the brain, causing the release of more oxytocin, further increasing uterine contractions. The process ends when the baby is born. Fruit ripening involves production of a plant hormone called ethylene. As the ethylene concentration increases, ethylene feeds back to tissue in the fruit, causing the release of more ethylene, which in turn enhances the ripening process.

Explain the difference between positive and negative feedback.

In positive feedback, the output of a system feeds back into the system, increasing the system's activity and output. Positive feedback drives a biological process (such as childbirth) to conclusion, after which the system shuts down. In negative feedback, the output of a system feeds back to the system in a way that decreases the system's output. Negative feedback is essential in homeostasis, returning a system to its set point.

Describe how epinephrine acts upon liver cells to mobilize glucose secretion during the fight or flight response.

In response to perceived threats (as part of the "fight or flight" response), cells in the adrenal glands (above the kidneys) secrete epinephrine into the bloodstream. Epinephrine is a protein hormone, and it binds with a G-protein coupled receptor on liver cells. Binding of epinephrine with the receptor induces a conformational change in the cytoplasmic side of the receptor (also known as its intracellular domain). This change enables the receptor to bind with a G protein, a membrane bound protein that's bound to the cytoplasmic side of the membrane. Binding changes the shape of the G protein so that it can discharge a molecule of GDP, and bind instead with GTP. Binding with GTP activates the G protein. In its activated state, the G protein moves along the cytoplasmic side of the membrane until it encounters a membrane-bound enzyme called adenylyl cyclase. This activates adenylyl cyclase, which converts a molecule of ATP into cyclic AMP (cAMP). cAMP now acts as a second messenger. It binds with proteins called kinases, which activate other kinases in what's called a signal transduction cascade. Because cAMP and the kinases that it activates can each act upon more than one substrate, the result is signal amplification. By the end of the process, millions of target molecules (the last molecule in the phosphorylation cascade is the target) are activated. In this case, the target is glycogen phosphorylase, an enzyme that breaks glycogen (a polysaccharide that's almost identical to starch) into glucose. The glucose diffuses from the liver into the bloodstream, where it can assist the skeletal muscles as they carry out the fight or flight response.

Describe the basic chemistry, overall structure, and biological importance of lipids.

Lipids are molecules that are either non-polar, or have large nonpolar regions. Many lipids are built of one or more fatty acids, which are hydrocarbon chains that terminate in a carboxyl group. Lipids are used for energy storage, for waterproofing, as essential components of cell membranes, and as building blocks for steroid hormones.

List the four key types of lipids. Briefly describe the function of each.

Lipids include triglycerides (fats and oils), which are used for energy storage and insulation; waxes, which are used for waterproofing; phospholipids, which are the key structural components of cell membranes; and steroids, which are signaling molecules (steroid hormones).

Explain why energy is essential to life.

Living things are complex, low entropy, systems. Generating and maintaining that complexity, pushing back against the increase in entropy that characterizes the universe, requires a constant flow of free energy. Because of the second law of thermodynamics (the idea that in any system, entropy increases over time), living systems need to take in more energy than they consume (with the difference being lost as heat that dissipates away into the environment).

Explain how energy capture and use are organized in living systems. List some examples.

Living things channel flows of free energy into sequential metabolic pathways that are optimized for efficiency. Within these metabolic pathways, energy is harvested or expended in many small, connected steps in which the product of one reaction becomes the reactant for the next reaction. Specific examples of these metabolic pathways include the reactions of glycolysis, the krebs cycle, the electron transport chains of cellular respiration and the light reactions of photosynthesis, and the Calvin Cycle.

Compare and contrast dehydration synthesis and hydrolysis.

Living things combine monomers into polymers through enzyme-catalyzed dehydration synthesis reactions. In these reactions, a hydroxyl group (an -OH) is pulled off of one monomer (or a group of already connected monomers), and a hydrogen atom is pulled off the other. The -H and -OH combine to form water (hence, dehydration synthesis, because it involves removing a water molecule). When living things digest or recycle polymers, they use the opposite process: enzymes insert a water molecule between the monomers making up the polymer. This breaks the bond that held the two monomers together. This process is called hydrolysis ("breaking with water").

Define "local regulator", and list some examples of cell communication by local regulators

Local regulators are signaling molecules that exert their effect over short distances (but without the cells touching one another). The "local" designation is intended to distinguish local regulators from endocrine glands, which release their signals (hormones) into the blood, and can have an effect in the most distant parts of the body. One example of a local regulator would be a neurotransmitter, a substance that is released from a presynaptic neuron and which diffuses across a tiny gap called a synapse. On the other side of the synapse is a target cell (a nerve, muscle, gland, etc). with receptors for the neurotransmitter. Another local regulator would be a morphogen involved in embryonic development. These morphogens are synthesized and released in one group of cells, and then diffuse to nearby cells, activating genes or even inducing apoptosis.

Describe the structure and function of lysosomes.

Lysosomes are membrane-bound organelles that contain hydrolytic enzymes. They're only found only in animal cells; (while plant vacuoles play similar roles, the two are considered to be distinct organelles). One function of the lysosome is intracellular digestion. After a cell ingests a particle by endocytosis, the particle will be enclosed in a vesicle, which will fuse with a lysosome. The lysosome will digest the particle. Lysosomes also recycle worn out, damaged, or excess organelles and molecules. They also play a key role in apoptosis (programmed cell death (discussed in another card).

What is membrane potential? How do cells create membrane potential, and what do they use it for?

Membrane potential is electrical charge across a membrane. Cells create membrane potential by pumping ions across their membranes. For example, mitochondria use energy from food to pump protons from the mitochondrial matrix to the intermembrane space. This gives the intermembrane space a positive charge relative to the matrix, and creates an electrochemical gradient that pulls these trapped protons through an ATP synthase channel back to the matrix, generating ATP. A homologous process using the same mechanisms occurs in the thylakoids of chloroplasts: the only difference is that the protons are pumped into the thylakoid space, rather than the intermembrane space. In nerve cells, the sodium-potassium pump pumps sodium ions out of the cell, and potassium ions into the cell. This creates membrane potential across the membrane. During an action potential, ions are allowed to flow down their concentration gradient, creating nerve impulses.

Describe the structure and function of mitochondria. Focus on how this structure relates to ATP synthesis.

Mitochondria are double-membraned organelles. That means that they have an outer cell membrane, and and an inner cell membrane. The inner membrane is highly folded, an adaptation for increasing surface area. The inner membrane is also where membrane-embedded enzymes take energy from electrons that originate in food, and use that energy to pump protons from the matrix (the region inside the inner membrane) to the intermembrane space (the space between the inner and outer membranes). This creates a proton gradient that forces protons to diffuse from the intermembrane space back to the matrix via a channel called ATP synthase. During this passage, ATP synthase uses diffusing protons' kinetic energy to convert ADP and Pi into ATP (the details of which are covered in another card). The matrix is, essentially, the cytoplasm of the mitochondria. Within the matrix, the reactions of the Krebs cycle occur. Mitochondria also contain their own DNA and ribosomes, a vestige of their origins as free living bacteria, acquired through endosymbiosis in a singular event that led to the origins of eukaryotic cells.

Using pH and temperature as examples, describe how enzyme activity is affected by changes in an enzyme's environment. Include the concept of "denaturation" in your answer.

Most enzymes have a pH optimum where they operate at peak efficiency. As the pH moves above or below the optimum, enzyme performance drops. A graph of enzyme efficiency plotted against pH shows a peak at the optimum, and then a drop off at either side. In terms of temperature, enzyme activity tends to increase with temperature, because more kinetic energy increases molecular motion and increases the chance that the enzyme will bind with its substrate(s). At a certain temperature, however, the amount of kinetic energy will disrupt the enzyme's internal bonds, changing the enzyme's shape in a way that leads to denaturation (disrupting the enzyme's catalytic abilities). A graph of enzyme and temperature shows a line that slopes upward with temperature until it reaches an optimum, and then a steeply sloping decline as the enzyme reaches the denaturation point. Note that this denaturation can be reversible or irreversible. In reversible denaturation, a restoration of optimal conditions will restore the enzyme's function as it regains its optimal shape. In irreversible denaturation, the enzyme's shape is permanently changes, and its catalytic ability is destroyed.

How do organisms transport large molecules across cell membranes?

Movement of very large molecules or other particles across the plasma membrane occurs through bulk transport, a type of process that involves large scale movements of the membrane, and which requires expenditure of cellular energy. In exocytosis, cells dump the contents of vesicles outside of the cell. In endocytosis, the membrane buckles in a way that surrounds a molecule, a particle, or some extracellular fluid, creating a cavity that becomes a vesicle. Endocytosis can be subdivided into several types: - In pinocytosis, the membrane pinches in. The pinching in continues until a vesicle forms, surrounding some of the extracellular fluid and whatever was inside it. Think of pinocytosis as the cell taking a small "sip" of the material outside the membrane. - In receptor-mediated endocytosis, a piece of the membrane pinches in response to some molecule that binds with a receptor embedded in the membrane. - During phagocytosis, the cell uses its membrane to surround a particle (or even another cell). The membrane pinches in to form a vesicle which enters the cytoplasm. Phagocytosis is used by white blood cells in the immune response to swallow invaders. Single celled organisms like amoebas use phagocytosis to eat.

Use the relationship between surface area and volume to explain why cells are small.

Needed substances, such as glucose and oxygen, enter cells by diffusing in through the cell's membrane, and then diffusing throughout the cell's volume. Metabolic wastes (like carbon dioxide) are generated inside the cell, and can only leave by diffusing from wherever they're generated through the membrane. Cells need to be small in order to have sufficient membrane surface area to allow for efficient diffusion of substances in and out. Small size is required because as an object gets larger, the amount of surface area it has relative to its volume decreases. For example, think of a cubical cell that's 1 unit in length. Its surface area is 1 x 1 x 6 (six square units of surface area); while its volume is 1 x 1 x 1 (1 cubic unit of volume) so its surface area to volume ratio is 6:1. Increase that cell's length to 10 units, and its surface area is now 10 x 10 x 6 (600 square units of surface area, and its volume is 10 x 10 x 10 (1000 cubic units of volume). The larger cell's surface area to volume ratio is 0.6:1. In other words, the larger cell's surface area to volume ratio is 1/10th that of the smaller cell. With such a small amount of surface area relative to its volume, a large cell can't efficiently use diffusion to get the nutrients it needs, and to release wastes.

Describe the biological importance of nitrogen.

Nitrogen is a key part of proteins, making up a central part of the amino group found in every amino acid. Nitrogen is also in the nitrogenous bases that make up nucleotides, the monomers of the nucleic acids DNA and RNA. Note that one of these nitrogen-bearing nucleotides is ATP, life's energy transfer molecule. Nitrogen can be a key limiting factor in ecosystems. While molecular nitrogen (N2) makes up most of the atmosphere, few organisms can directly absorb nitrogen. The main organisms that do this are nitrogen-fixing bacteria, many of which have symbiotic relationships with plants.

Explain the basis of directionality in nucleic acids, and why that's biologically important.

Nucleic acids (DNA and RNA) consist of linear sequences of nucleotides. Within each nucleotide, the 5' carbon in the nucleotide sugar (deoxyribose or ribose) binds with a phosphate group. That phosphate group binds with the 3' carbon on the next nucleotide sugar in the chain. The enzymes that build nucleotide chains are called polymerases, and their active site is structured in such a way that they can only add new nucleotides to the 3' end of a growing nucleotide strand. Another way to say this is that nucleic acids are always synthesized in a 5' to 3' direction. This limitation structures the entire process of DNA replication (described in another card). It also explains why eukaryotes, with their linear chromosomes, need to have telomeres: that's because a few nucleotides get lost from the 3' end of a DNA strand in every replication cycle.

Describe the biological importance of nucleic acids.

Nucleic acids are life's key informational molecules. They are polymers of nucleotides (the structure of which is covered in another card). DNA is the molecule of heredity. It's the repository of genetic information, and the informational component of the chromosomes that get passed from one generation to the next during reproduction, and from mother cell to daughter cells during growth and development. RNA is a hereditary molecule in some viruses, but more frequently is involved in information transfer, as in the messenger RNA that carries a genetic message from chromosomes to ribosomes, where these messages are converted into protein. RNA can also be an action molecule with catalytic properties. Such catalytic RNAs include ribosomes (which translate RNA instructions into proteins) and spliceosomes, which edit eukaryotic RNA so that it can be translated into protein. In addition, ATP is a nucleotide monomer (a monomer of RNA). ATP is life's key energy transfer molecule, powering most cellular work.

Describe the biological importance of oxygen.

Oxygen is a key part of almost all biological molecules. Oxygen is required for aerobic cellular respiration, during which oxygen acts as the final electron acceptor. The free oxygen (molecular O2) in our atmosphere wasn't present on the early Earth; it was released into the early seas by photosynthetic cyanobacteria which split apart water molecules to gain electrons, releasing O2 as a by-product. When the seas became oxygen saturated, O2 bubbled into the atmosphere. It's possible that the development of multicellular life about 600 mya (million years ago) was made possible by the accumulation of atmospheric oxygen to a certain concentration that made multicellularity possible. By about 400 mya accumulation of oxygen in the atmosphere led to the formation of an ozone layer, which blocks the sun's ultraviolet rays, making life on land possible.

Compare and contrast active and passive transport. As you do, explain what powers each process.

Passive transport is transport that allows molecules or ions to follow their diffusion gradient, diffusing from high concentration to low concentration. Passive transport relies on the kinetic energy in the diffusing molecules or ions, and doesn't require any metabolic energy to be expended by the cell. Active transport involves pumping a molecule or ion up its concentration gradient, from lower concentration to higher concentration. This requires energy on the part of the cell. This energy can be supplied by conversion of ATP to ADP to power the pumping process (which is how the sodium-potassium pump is powered in nerve cells), or by electron flow (as in the proton pumps used by chloroplasts and mitochondria to power ATP synthesis).

Describe the role of phospholipids in cell membranes.

Phospholipids form the basic structure of the membrane. This function emerges from their chemical structure. Phospholipids have a hydrophilic, phosphate-bearing head, and a hydrophobic tail consisting of two hydrocarbon chains. When mixed with water, phospholipids will spontaneously self-organize into several configurations, one of which is a bilayer: the basic structure of a biological membrane. In a membrane bilayer, two layers of phospholipids form a structure in which the hydrophobic fatty acid tails create a water free zone (the inside of the membrane), while the hydrophilic heads face outwards toward the watery environment outside of the cell, and the cell's watery, cytoplasmic interior. This structure is further stabilized by weak bonds between the hydrophobic tails (called London dispersion forces).

Describe the structure of phospholipids, and explain the relationship between phospholipid structure and the role that these molecules play in cell membranes.

Phospholipids have a polar, hydrophilic head; and a non-polar, hydrophobic tail. The central molecule in a phospholipid is a 3 carbon alcohol called glycerol (the same molecule found in fats and oils). Bonded to the glycerol on one side are two fatty acids, forming the hydrophobic tail. On the other side of the glycerol is the hydrophilic head, which contains a negatively charged phosphate group. Because of this structure, phospholipids can spontaneously form a phospholipid bilayer. In a phospholipid bilayer, the there are two rows, or layers. In each row, the hydrophilic heads face out (interacting with water molecules), while the tails face inward, forming a water-free zone. In addition, the tails are attracted to one another by very weak intermolecular forces (called London Dispersion forces, or hydrophobic bonds). Now imagine this bilayer forming a sphere. Outside of the sphere is the watery exterior. Inside is the watery interior. That bilayer is the framework of the cell membrane. Note that phospholipids form the basis of cell membranes in two of life's three domains: bacteria and eukarya (eukaryotes). Archaea use a different lipid to form their cell membranes.

Describe the biological importance of phosphorus and sulfur.

Phosphorus, as part of a phosphate group (-PO4), plays roles in energy transfer and information transfer. Living things energize molecules (such as ADP) by adding phosphate groups to them (creating, in this example, ATP) . Transferring phosphate groups releases energy that can power cellular work (which occurs when ATP is broken down to ADP and Pi (inorganic phosphate). Phosphate groups are part of the sugar-phosphate backbone of life's key informational molecules, DNA and RNA. Phosphate groups also play a key role in the structure of phospholipids, the key structural molecules in cell membranes. Because of phosphorus' importance, it's often a key limiting nutrient in ecosystems. Pollution of waterways with phosphate, caused by runoff from farms or improperly treated wastewater, can cause blooms of algae resulting in eutrophication. Sulfur is a key part of of the structure of proteins. Two amino acids, methionine and cystine, contain sulfur. Covalent bonds can form between spatially adjacent sulfhydryl groups in cysteine residues in a polypeptide. This creates a disulfide bridge, which is a key part of the tertiary structure of proteins.

Describe the chemical composition and the function of the plant cell wall.

Plant cell walls are composed primarily of cellulose, a polysaccharide. The wall provides a permeability barrier for some substances, but its major function is to serve as a kind of pressure vessel: a rigid boundary that prevents the cell from over-expanding in response to osmotic pressure as water flows into a cell, causing it to expand. This maintains turgor pressure, keeping plant cells firm and preventing plants from wilting. The cell wall also plays a key structural role in plant stems, making up wood and xylem, the conductive tubes that allow water to move up a plant stem.

Describe how cell communication via cell-to-cell contact occurs in plants.

Plant cells can directly communicate via plasmodesmata. These are gaps in the cell walls of adjacent cells. These gaps allow the cell membranes of adjacent cells to form an open channel through which cytoplasm can flow, allowing for passage of molecules and ions from cell to cell, including ions and molecules that serve as cell signals.

Explain how the structure and function of proteins emerges from interactions between the amino acids making up that protein.

Protein structure and function emerges from at least three and often four types of interactions between the amino acids that make up a protein. The first level of structure is primary structure: it consists of the sequence of amino acids in a polypeptide chain. This sequence is genetically determined, and emerges as ribosomes translate messenger RNA into polypeptide chains, with each amino acid's position and identity spelled out by codons (3 base sequences) in mRNA. Secondary structure involves interactions between carbonyl groups and amino groups in the polypeptide backbone. These interactions can cause a polypeptide to twist into a coiled alpha helix, or form a regularly folded structure called a pleated sheet. Interactions between amino acid side chains (also called R-groups) result in a tertiary structure. These interactions involve hydrogen bonds, ionic bonds, covalent bonds or hydrophobic clustering. The result is a complex, three dimensional shape. Multiple polypeptides can interact to form a quaternary structure, which is found in proteins such as hemoglobin, which consists of four, interconnected, polypeptides. The bonds that stabilize a quaternary structure include hydrogen bonds, ionic bonds, and hydrophobic interactions.

Name the monomer of proteins, and describe that monomer's structure.

Proteins are polymers of amino acids. Amino acids are built around a central carbon, attached to amino groups, carboxyl groups, a hydrogen atom, and a variable R group. The R group, also called a "side chain" can be polar, non-polar, acidic, or basic. Interactions between amino acids (covered in another card) determine the protein's three dimensional shape.

Describe the biological importance of proteins.

Proteins are the most diverse macromolecule Their functions include - catalysis (as enzymes); - structure (as in the flexible protein collagen or the more fibrous keratin, which makes hair, feathers, and nails; energy storage (albumin); - motion (as in the proteins actin and myosin, which interact to create contractile muscle tissue); - transport (as in hemoglobin, which carries oxygen); and - information transfer (as in protein hormones like insulin or protein neurotransmitters like serotonin).

Describe how proteins fit into the cell membrane.

Proteins can embed into the membrane in several ways. Some proteins are transmembrane proteins: these have a hydrophobic core that fits into the nonpolar inner portion of the membrane, with hydrophilic regions extending into the cytoplasm below and the membrane exterior above. Other proteins might have a nonpolar region that embeds into the hydrophobic membrane middle, with a single hydrophilic region that juts into the cytoplasm or cell exterior. Other proteins are peripheral, attaching to phospholipid heads that are either on the cytoplasm side of the membrane, or the cell exterior.

Explain the function of the contractile vacuole in freshwater protists.

Protists in freshwater are hypertonic to their freshwater environment. As a result, water moves into these cells by osmosis. To osmoregulate, many protists contain an organelle called a contractile vacuole. This organelle fills with water, and then contracts to expel water from the cell. If the environment becomes more hypertonic (diminishing the water potential gradient) the cell can adapt by decreasing its rate of contractile vacuole contraction, and do the reverse in more hypotonic environments.

What is quorum sensing?

Quorum sensing is a process by which organisms restrict the expression of certain genes until cell density reaches a certain level. That's because only at that level will the phenotype that results from the expression of these genes be beneficial. Use of quorum sensing has been documented in bacteria, plants, and social insects (but might be more widely used). An example of quorum sensing involves bacterial formation of biofilms, a matrix of extracellular polymers that improve the ability of bacteria to stick to a substrate (such as your teeth, where they contribute to the formation of dental plaque). As the bacteria form a biofilm, they use quorum sensing to to determine when to secrete molecules that provide them with increased virulence and antibiotic resistance, and when to form spores that would enable them to create additional bacterial colonies.

Describe the structure, function, and evolutionary importance of ribosomes.

Ribosomes are particles composed of ribosomal RNA and protein. Ribosomes consist of large and small subunits that join together during protein synthesis. The function of ribosomes is to read a genetic message encoded in a sequence of mRNA nucleotides, and to translate that message into a sequence of amino acids that make up the primary structure of a protein. Evolutionarily, ribosomes are basic to all life; LUCA (the last universal common ancestor) was a cell with ribosomes. The structure of ribosomes is one piece of evidence that points to a great evolutionary divide among living things. Analysis of the rRNA making up ribosomes indicates that life consists of three great domains: bacteria, archaea, and eukarya. The archaea, based on rRNA sequences and other features, are more closely related to the eukaryotes than to the bacteria. Another way to think of this is that prokaryotes, a taxon that includes bacteria and archaea, is a polyphyletic group.

List some of the cellular responses that can be elicited by signal transduction pathways, and provide specific examples.

Signal transduction pathways can result in enzyme activation (epinephrine acting upon liver cells), cell division (cytokines from helper-T-cells causing B cells to mature into a clone of plasma cells), changes in gene expression (various morphogens activating homeotic genes during development), and apoptosis (caused in a variety of circumstances, including during development).

Describe the structure and function of steroids and waxes.

Steroids consist of four or five fused carbon rings, often with hydrocarbons attached. They're the starting point for steroid hormones (important signaling molecules). Cholesterol is a steroid that plays a stabilizing role in cell membranes. Waxes consist of two or more hydrocarbon chains that are bonded together. They play an important waterproofing role, especially in leaves, where waxes coat the surface of leaves, where they reduce water loss.

Where does the Calvin-Benson cycle occur, what does it produce, and how?

The Calvin-Benson Cycle occurs in the stroma (the fluid in between the thylakoids and the chloroplasts' inner membrane). Using the products of the light reactions (ATP and NADPH) and carbon dioxide, the cycle creates the reduced 3-carbon compound G3P, which is converted by other enzymes into carbohydrates (or anything else a plant cell needs). The cycle has three primary phases. During the carbon fixation phase, carbon dioxide is combined with a five carbon molecule called RuBP. This reaction is catalyzed by the enzyme RuBisCo. The six carbon product of this reaction immediately dissociates into two 3 carbon molecules. During the investment and harvest phase, these three carbon molecules are reduced and phosphorylated into six molecules of glyceraldehyde-3-phosphate (also known by the acronym G3P or PGAL, which stands for phosphoglyceraldehyde). The chemical energy for this comes from the ATP and NADPH that were generated during the light reactions. One of these G3Ps is then harvested (removed from the cycle). The last phase is regeneration of RuBP. During this phase, the remaining five G3Ps are rearranged into three RuBPs, the compound that acts as one of the substrates during the carbon fixation phase (the other substrate being carbon dioxide).

Describe the structure and function of the Golgi complex.

The Golgi complex consists of a series of membrane-bound flattened sacs. The Golgi receives vesicles from the rough and smooth ER, and chemically modifies the contents of these vesicles (usually proteins). Once these proteins are modified, they're packaged into vesicles that bud off from the outer side of the Golgi, and sent to organelles, to the cell membrane, or exported from the cell. For example, proteins that serve as membrane biomarkers (such as the "A" and "B" glycoproteins on red blood cells) are marked as such by the attachment of short polysaccharide chains. This process (called glycosylation) occurs in the Golgi complex. Note that the Golgi complex is also called the Golgi body, or the Golgi apparatus.

Explain solute potential and its formula: ΨS = - iCRT

The formula for water potential is Ψ = ΨS + ΨP. In this formula, ΨS represents solute potential. Adding solute to a body of water increases its solute potential, but increasing solute potential decreases overall water potential. In other words, water will move from areas of lower solute potential to areas of higher solute potential. The way to keep this straight is to connect "higher solute potential" with "hypertonic." Water flows from hypotonic to hypertonic. In the same way it flows from a solution with less water potential to one with higher solute potential. Conversely, when you see "lower solute potential" you can think "hypotonic." Solute potential has several components. You don't, for the purposes of the AP exam, need to memorize the formula, but you might be required to plug some numbers in. Here's what you need to know. - i is the ionization constant. It's the number of particles a solute will make in water. A salt like NaCl will dissociate into two ions, giving it an ionization constant of 2. A molecule of glucose doesn't dissociate, giving it an ionization constant of 1. - C is the molar concentration, which you determine in two steps. First, determine the molecular weight of your solute. To do this, you divide the weight of the solute by the molecular weight of the compound. For example, if you have 100 grams of glucose (C6H12O6: molecular weight = 180.165g/mole) then you'd divide 100 grams by 180.165 g/mole to get 0.552 moles. Second, figure out the molar concentration in g/Liter. If you were dissolving 0.552 moles of glucose in 2 liters, you'd have a molar concentration of 0.552 moles/2 liters = 027 g/Liter, or a 0.27 M solution. - R is the pressure constant. This is 0.0831 bars at room temperature. - T = temperature in Celsius, plus 273 (to get degrees above absolute zero).

As an example of cell communication, describe how cell communication via cell to cell contact occurs in the immune systems' humoral response.

The immune response is based on a series of cell to cell messages. As an example, let's explain the cellular communication that leads B cells to mature into antibody-secreting plasma cells, a key part of the specific immune response. The process begins with a macrophage: a sentinel cell that patrols the body tissues searching for invading pathogens (disease causing agents). Once a macrophage encounters a pathogen, it devours it and digests it. Following digestion, the macrophage will display some unique molecules from the pathogen in its Class II major histocompatibility complex protein, a membrane protein. At this point, the displayed piece of the pathogen can be called an antigen (an antibody generator). Next, the macrophage moves to a lymph node. There, the macrophage will present the antigen to Helper T cells: essentially the macrophage is holding the antigen aloft, and saying "look what I found." Each Helper T cell tests the antigen by contacting it with a T cell receptor. If the Helper T cell's receptor doesn't complement the shape of the antigen, it moves on allowing another helper T cell to try. Presentation continues until the macrophage encounters a helper T cell with a T cell receptor that closely complements the shape of the antigen. Once a match is found, the macrophage and helper T cell will grab on to one other using binding proteins, and then secrete chemical messages called cytokines, which induce the helper T to clone itself. These helper Ts, now numbering in the millions, wait in the lymph node until they encounter a B cell that has independently encountered the same pathogen, and has a receptor that binds with antigen from that pathogen. Once the Helper T cell meets with this B cell, it sends cytokines to the B cell, causing the B cell to clone itself and to differentiate into an antibody secreting plasma cells. These cells release antibodies, proteins that bind with the antigen, helping to neutralize and destroy the pathogen that the antigen belongs to.

Where do the light-dependent reactions of photosynthesis occur? What do these reactions produce, and how?

The light-dependent reactions of photosynthesis convert the energy in light into the chemical energy of NADPH and ATP. These reactions occur in two photosystems that are located the thylakoid membranes within chloroplasts (and homologous structures in Cyanobacteria). Photoexcitation of chlorophyll molecules in Photosystem II begins a flow of electrons along an electron transport chain in the thylakoid membrane. This flow of electrons powers proton pumps, which pump protons from the stroma to the thylakoid space, creating a chemiosmotic gradient that powers ATP synthesis as protons diffuse from the thylakoid space back to the stroma via an ATP synthase channel. This proton gradient is enhanced as the chlorophylls in PS II oxidize water molecules in order to replace their lost electrons. This oxidation of water results in production of oxygen gas as a byproduct of the light reactions. Photoexcitation of chlorophylls in Photosystem I, which follows Photosystem II, creates another electron flow. These electrons flow to the enzyme NADP+ reductase, which reduces NADP+ into NADPH. In the Calvin Cycle that follows, the NADPH and ATP from the light reactions will be used to power the creation of carbohydrates from carbon dioxide.

Explain how the mitochondrial electron transport chain generates ATP.

The mitochondrial electron transport chain begins with oxidation of the two products of the Krebs cycle, NADH and FADH2. Oxidizing these molecules liberates energetic electrons, which flow along the mitochondrial electron transport chain, a series of membrane embedded enzymes located on the mitochondrial inner membrane. Some of these enzymes are proton pumps, and they use the energy of these flowing electrons to pump protons from the mitochondrial matrix to the intermembrane space (the space between the mitochondrial inner and outer membrane). The concentration of protons in the intermembrane space creates an electrochemical gradient. The only way the protons can leave this space is through the ATP synthase channel. This channel allows protons to diffuse back to the the matrix, and as protons move through ATP synthase, their kinetic energy powers a conformational change in binding sites in ATP synthase that enables this enzyme to combine ADP and inorganic phosphate, creating ATP. Just remember these lyrics: The mitochondrial electron transport chain Uses electron energy for pumping protons From the mitochondrial matrix to the intermembrane space Increasing proton concentration in that place, The only way the protons can escape Is through a channel and an enzyme, ATP synthase. Which uses diffusing protons' kinetic energyTo make ATP, from ADP and P

Name the monomer of nucleic acids, and describe this monomer's structure. Describe how these monomers are different in DNA and RNA.

The monomers of nucleic acids are nucleotides, which consist of a 5 carbon sugar, a phosphate group, and one of four nitrogenous bases. The phosphate group is connected to the 5' carbon in the sugar, and the nitrogenous base is connected to the 1' carbon. In DNA, the sugar is deoxyribose, and the bases are adenine, thymine, cytosine and guanine. In RNA, the sugar is ribose, and the bases are adenine, uracil, cytosine, and guanine.

Cellular respiration can be used to generate heat instead of ATP. Explain.

The process by which respiration generates heat instead of ATP is called non-shivering thermogenesis. Here's how it works. Newborn and hibernating mammals have a type of fat called brown fat. As opposed to white fat (the kind in a steak, or on our own adult bodies), brown fat cells are dense with mitochondria (which is why it's brown). When the animal needs to generate body heat, hormonal signals induce a proton channel called thermogenin to form in the inner mitochondrial membrane. This channel lets protons diffuse back to the matrix from the intermembrane space, without generating ATP. However, the flow of electrons in the electron transport chain generates heat: just imagine electricity flowing through the high resistance wire in a toaster, and you'll have the idea.

List the six key elements in living things.

The six key elements in living things are C, H, N, O, P, and S.

What is the standard error of the mean? How does it relate to 1) error bars, 2) confidence intervals, and 3) interpretation of statistical results

The standard error of the mean tells you (and is calculated from) two things: 1) the standard deviation of a set of data points in a sample size, which means how widely the data in a sample was dispersed around the mean; and 2) the sample size. Put those together, and what you get is a confidence interval: a a range of values that's likely to encompass the true value in your set of data. For example, imagine a study that's testing the level of total cholesterol in a sample of patients who are taking a certain medication. The data might be expressed as 180 ± 15 mg/dL. That's saying that the mean is 180, and that the spread of values for a sample of this size might have been 15 units above or below the mean.When you represent this data in a bar graph, you'd draw the data with an error bar that goes 15 units above the mean, and 15 units below. When you interpret results, the size of the error bar represents the statistical significance of the data. For example, if the data set from treatment A is the one above (180 ± 15 mg/dL) and data set from treatment B is 170 ± 10 mg/dL), then you can't say that the two treatments are producing statistically significant results, because the error bars (or confidence intervals) overlap. If, in a second experiment, treatment A resulted in 180 ± 15 mg/dL treatment B is 150 ± 10 mg/dL), then the results are statistically significant.

Cell signaling involves 3 key phases. Using the example of a polar signaling molecule (one that can't diffuse across the membrane), briefly describe what happens in each phase.

The three phases of cell signaling are 1) reception; 2) signal transduction (often with signal amplification); and 3) cellular response. Reception begins as a receptor molecule embedded in the cell membrane binds with a signal molecule (also called a ligand). This binding is based on complementary shape, and is as specific as the relationship between an enzyme and its substrate. Next is transduction. Binding of the ligand with the receptor induces a conformational change in the receptor on its cytoplasmic side, which activates a second messenger, often cyclic AMP. This phase is called transduction because the 1st message has now been transduced into this new form (the molecules that make up the second messenger). The third phase is response. The second messenger interacts with molecules in the cytoplasm in a way that amplifies the signal, culminating in a cellular response. Often, amplification involves a phosphorylation cascade, a kind of molecular chain reaction in which a small number of second messengers activate many intermediates, each of which activates many enzymes.

*The second law of thermodynamics says the entropy increases over time. How can life, with its highly ordered systems, exist?

The universe began as a very low entropy system. Over time, (since the Big Bang) entropy has been increasing. Life, with all of its complexity, is able to exist because living systems couple available flows of free energy (such as the light emitted from the sun) to processes that create ordered, self-replicating systems. In other words, life is a little current of order in the overall flow of entropy that characterizes the universe. This works because living things are open systems. As free energy flows through them, organisms couple their use of free energy into processes such as growth and development, maintaining homeostasis, repairing themselves, and reproduction. Photosynthetic organisms are able to directly power these processes by sunlight. Heterotrophs need to access free energy in chemical form (food created by autotrophs) in order to power their life processes. In both cases, enormous amounts of waste and waste heat are produced, and overall entropy increases. If the sun were to stop shining, the main source of free energy that sustains these activities would come to an end, as would all of life.

What does a χ2(Chi square) test enable you to evaluate? In your answer, explain the idea of a null hypothesis, and what it means to accept or not accept a null hypothesis.

The χ2 test allows you to determine whether the difference between observed results and expected results is statistically significant. If the results are not significant, then you can accept a "null hypothesis." Accepting the null hypothesis means that the difference between expected and observed results is not significant. If, on the other hand, you can't accept the null hypothesis, it means that your expectation (hypothesis) was wrong, or that there was a problem with your experimental methods, data collection, etc.

What are monomers? How do they connect to form polymers?

Three of the four macromolecule families that make up living things — carbohydrates, proteins, and nucleic acids — are built from smaller building blocks called monomers. These monomers are, respectively, monosaccharides, amino acids, and nucleotides. Living things build macromolecules with specific three dimensional shapes and functions by combining monomers into polymers through a process called dehydration synthesis.

Explain how cells control what diffuses across their membranes.

To begin with, there are some types of molecules that cells don't control. For example, biological membranes allow small nonpolar molecules such as carbon dioxide, nitrogen, and oxygen to freely diffuse across the membrane's phospholipid bilayer, following their diffusion gradient. That's called simple diffusion. However, polar molecules and ions won't diffuse through a phospholipid bilayer. To allow their diffusion, cells have protein channels: transmembrane proteins that only let specific molecules or ions pass, depending on the cell's needs. This is called facilitated diffusion.

Describe the structure and function of vacuoles.

Vacuoles are membrane bound organelles, generally used for storage. Plant cells contain a large central vacuole which stores water, and which also has a variety of other functions, including storing and releasing needed macromolecules, sequestering waste products, and maintaining turgor pressure.

Explain how hydrogen bonds come about from water's chemical structure, and describe hydrogen bonds.

Water is a polar covalent molecule. Because oxygen's nucleus has eight protons while hydrogen's nucleus has one, the electrons shared by the two hydrogen atoms and the one oxygen atom in a molecule of water are shared unequally. The negative electrons cluster around the oxygen side of the molecule, giving that side of the molecule a partial negative charge. In contrast, the region with the hydrogen atoms gains a partially positive charge. Hydrogen bonds are intermolecular bonds that form between the partially positive (hydrogen) side of one water molecule and the partially negative (oxygen) side of another water molecule. Hydrogen bonds can also form between positive and negatively charged regions of other molecules, such as between the complementary bases in DNA (where adenine bonds with thymine, and cytosine with guanine).

How does water pass through a cell membrane?

Water is a polar molecule, and polar molecules, in general, can't diffuse through the lipid bilayer. But because water is a small molecule, small amounts of it can diffuse through the phospholipid portion of the membrane. In addition, to facilitate water's passage through the membrane, cells produce channels called aquaporins: selective protein channels for water diffusion.

Describe the structure of leaf stomata, and explain how guard cells help plants limit excessive water loss.

Water is moves from a plant's roots up to its shoot through a process called evapotranspiration, which pulls water up the stem of a plant as water evaporates from a plant's leaves. The water evaporates through pores called stomata on the underside of leaves, which are otherwise impermeable to water because of a waxy cuticle on the leaves' upper and lower epidermis. The stomata is formed by cells called guard cells. These cells, when they have sufficient water, buckle outward, creating a pore that allows carbon dioxide to enter into the leaf for photosynthesis, but which, as an unavoidable consequence, also allows water vapor to escape. When a plant has insufficient water, guard cells lose water and straighten out, closing the stomata, which traps water inside the leaf. While this reduces (or stops) photosynthesis, it also keeps the tissues of the plant from being damaged by dehydration. Cells in leaves can regulate whether the nearby stomata are open or closed. When water is available, nearby cells pump potassium ions into guard cells. Water follows by osmosis, causing the guard cells to buckle and open. When water is scarce, this pumping stops. Potassium ions flow out of the guard cells, and water follows, causing the stomata to close.

What is water potential?

Water potential is a measurement of water's tendency to move from where it is to where it's not, as determined by variables such as solute concentration and pressure. The basic idea is that water will always flow from areas of higher water potential to areas of lower water potential. Water potential can be modeled by the formula Ψ = ΨS + ΨP (water potential = solute potential + pressure potential). We've already looked at Ψ, which is water potential, so let's look at ΨS and ΨP. ΨS is solute potential. Adding solute to a body of water decreases its water potential. If that body of water is adjacent to an area with higher water potential, then the water will flow from the area with higher water potential (with less solute) to the area with the lower potential (with more solute). This is exactly like how water will flow from a hypotonic area to a hypertonic area. Ψp is pressure potential. Adding pressure (like pressing on the plunger in a syringe) increases water potential, causing water to flow away from that higher pressure area toward an area with lower pressure (and lower water potential).

When graphing data, what's the relationship between a graph's X and Y axes, and the dependent and independent variables? While you're at it, compare and contrast the two types of variables in a controlled experiment.

When graphing data, the independent variable goes on the X axis, and the dependent variable goes on the Y axis. The independent variable can be a variable that you manipulate in an experiment (such as temperature, light intensity, concentration of a solute), or it can be time (which can't be manipulated, but can be controlled). The dependent variable is the measured outcome that's the result of the independent variable (growth, activity, etc.)

Explain how enzyme activity is affected by substrate concentration.

When substrate concentration is low, the probability of the enzyme bumping into the substrate in the right orientation for the active site to catalyze the reaction is low, and the product of the reaction will be produced at a low rate. As substrate concentration increases, the rate of the reaction will increase. At a certain point, however, the enzyme will reach a saturation point, where every enzyme's active site is filled with substrate, and the reaction will reach a maximum rate. A graph of enzyme function plotted against substrate concentration will show an upward sloping line that flattens out as the enzyme reaches its maximum rate.

Describe the importance of membrane proteins.

While phospholipids make up the structural framework of the membrane, many membrane function are only possible because of membrane proteins (which can outweigh the phospholipid portion by weight). Membrane proteins can act as - Channels or ports, allowing the cell to take in and let out molecules that cannot diffuse through the phospholipid bilayer portion of the membrane. - Carriers, allowing the cell to perform active transport, moving molecules from low concentration to high concentration. - Attachment points for the fibers of the cytoskeleton, allowing the cell to change its shape and move. - Membrane-embedded enzymes. These are involved in cell processes like photosynthesis, cellular respiration, and intracellular digestion. - Receptors, receiving chemical messages (including hormones) and relaying these messages into the cytoplasm.