AP bio test 2020

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 basic niche of viruses. 2. Describe the size and structure of viruses. 3) Compare the lytic and lysogenic viral life cycles (DNA viruses only: retroviruses are in another card).

1) Viruses are tiny, obligate, intracellular parasites that reproduce themselves by hijacking a host cell's metabolic machinery, and using it to replicate more viruses. 2) Viruses can be as small as 30 nanometers across. In comparison, DNA is 2 nanometers wide, and a cell membrane's lipid bilayer is about 8 nanometer wide. The structure of a virus consists of a core of genetic material (DNA or RNA) surrounded by proteins that form an outer protein coat. Some viruses have an additional phospholipid bilayer, usually stolen from the host cell. 3) In the lytic cycle, a virus lands on a cell's outer surface (the cell wall or membrane). Next, the virus injects its DNA into the cell's cytoplasm. The DNA is replicated using the cell's replication machinery (DNA polymerases and other enzymes). The host cell's RNA polymerases are used to transcribe and translate the viral DNA into the protein components that make up the virus's protein coat. The viral proteins and genetic material self assemble into new viruses. At a certain point, the host bursts open, releasing new viruses into the environment. In the lysogenic cycle, a virus injects its DNA into its host. Then the DNA incorporates itself into the host cell's chromosome. This viral DNA, once integrated into the host, is called a prophage or a provirus, depending on whether the host is a bacterium or a eukaryotic cell, respectively). Each time the host cell replicates itself, it also replicates the viral DNA. At a certain point, the prophage or provirus breaks out and initiates a lytic cycle, replicating many new viruses and destroying its host in the process.

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.

What's the connection between gene expression and phenotypic differences between cells?

A key idea in developmental biology is the idea of genomic equivalence. All cells in the same organism have the same DNA, derived from the zygote (fertilized egg). During the course of development, different genes get expressed. That difference in gene expression is what accounts for the differences among the cells of an organism. For example, the cells making up the lens of your eye possess the same DNA as the cells making up the muscle tissue in your biceps. The difference is that the eye lens cells express only eye-lens proteins, while muscle cells express an array of muscle tissue proteins.

What is a point mutation? Describe the three effects of substitution mutations.

A mutation is a change in a DNA sequence (or the entire structure of a chromosome, though that will be addressed in another card). A point mutation involves a change in a single base pair (for example, substituting an A for a G), a deletion of a base, or an insertion of a base. Because of the redundancy of the genetic code, many substitution mutations can be silent, which means that they don't change the amino acid that the gene is coding for. This is especially common when the substitution mutation is in the 3rd base of a triplet. A missense mutation changes the amino acid in a protein (for example, from glycine to alanine. A nonsense mutation changes a codon coding for an amino acid to one that codes for a stop codon.

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).

What is a promoter?

A promoter is a DNA sequence where RNA polymerase can bind to initiate transcription. The promoter is always upstream from the gene. Along with RNA polymerase, other transcription factors bind at or near the promoter region. These transcription factors play a regulatory role, enhancing or inhibiting gene expression.

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.

Describe adaptive melanism, and explain how mutations in the MC1R gene have led to adaptive melanism in mice.

Adaptive melanism is the darkening of skin, fur, scales, feathers or appendages (wings in insects, for example) within a population in response to darkening of the environment. It's not something that occurs in an individual (such a when a person's skin becomes more tan during the summer), but which occurs within a population, as its gene pool evolves in response to natural selection. The selective pressure that results in melanism is typically predation. Adaptive melanism has been documented in the rock pocket mouse, a species that lives in the American southwest. Populations of mice live on dark, igneous rocks formed from lava flows, or much lighter, sand-colored granite rocks. Because of predation by predatory birds, there's strong selective pressure for mice to blend in with the substrate they live on, and there's a high frequency of dark mice that live on the lava flows, and lighter colored mice on the granite rocks.

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.

What's an operon?

An operon is a group of genes transcribed in a single mRNA molecule, which can then be translated into multiple proteins, all of which are part of the same metabolic pathway or process. Operons are found in prokaryotes (and not in eukaryotes).

What is apoptosis? Define the term, and describe the two apoptotic pathway, and describe the overall mechanism behind the process.

Apoptosis is programmed cell death. Unlike necrosis, which results from traumatic injury to cells, apoptosis is a highly regulated process in which cells are broken down into cytoplasmic fragments called blebs that can be consumed by phagocytosis cells, preventing cellular debris from damaging nearby cells. Apoptosis can be initiated through one of two pathways. In the intrinsic pathway the cell destroys itself because it senses cell stress or damage (particularly to its DNA). In the extrinsic pathway the cell destroys itself because of signals from other cells. Both pathways induce cell death by activating caspases, which are proteases (enzymes that degrade proteins). The two pathways both start with activation of initiator caspases, which then activate executioner caspases, which then initiate a cascade of reactions that systematically render the cell into blebs.

Compare and contrast how genetic information is stored in bacteria and eukaryotes.

Bacteria generally store their DNA in looped chromosomes. Their genome size ranges from 100,000 to 10,000,000 base pairs. Bacterial DNA is "naked" (not wrapped around a protein scaffold). Eukaryotic DNA is organized into multiple linear chromosomes, which is wrapped up around histone proteins. Eukaryotic genomes are orders of magnitude larger than bacterial genomes. The human genome, for example, consists of 3.2 billion base pairs (but that is by no means the largest genome: some plant genomes range up to 150 billion base pairs).

What's the probability that in a family with five offspring, all of the children will be girls?

Because each birth is independent, you use the rule of multiplication. The probability of each child being a girl is 1/2. The probability of 5 children all being girls is 1/2 x 1/2 x 1/2 x 1/2 x 1/2 (the product of all of these individual probabilities). In this case, the product is 1/32.

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 during 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.

Explain the difference between an inducible and a repressible operon.

Both inducible and repressible operons are examples of "negative" gene regulation, because both work by turning off gene expression. Inducible operons (such as the lac operon) are turned "on" by the presence of a metabolite (a molecule that's part of a metabolic pathway; in this case, it's the disaccharide lactose). In other words, the default condition of the operon (meaning the transcription of its genes) is "off." When lactose diffuses into the cell, control mechanisms induce transcription of the genes for lactose digestion. When all the lactose is digested, the operon again switches off. Repressible operons (such as the trp operon) are turned "off" by the presence of a metabolite (in this case, the amino acid tryptophan). In other words, the default condition of this operon is "on:" when there's no tryptophan in the environment, the cell produces enzymes for tryptophan synthesis. But the presence of tryptophan in the environment turns transcription of the operon off.

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.

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

Carbohydrates, lipids, proteins, and nucleic acids.

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.

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.

Describe the structure of DNA, and explain how its structure allows it to serve as the molecule of heredity.

DNA is a double stranded molecule composed of nucleotide monomers. Each monomer consists of the 5 carbon sugar deoxyribose, a phosphate group, and one of four nitrogenous bases. Each strand of the double helix consists of covalently bonded deoxyribose sugars and phosphate groups, which comprise DNA's sugar-phosphate backbone, and which is indeterminate in length. The sugar is bonded to the nitrogenous bases, and these bases can bind with one another, connecting one strand to the second strand. This bonding follows base pairing rules. Specifically, adenine (a single ring purine) can bind with thymine (a double ring pyrimidine), and cytosine (a pyrimidine) can bind with guanine (a purine). The bases in DNA can occur in any order, and comprise an informational code which specifies the sequences of molecules of RNA and protein, both of which work to carry out the activities that make life possible. The bonds between the bases are hydrogen bonds, and these bonds can be easily separated by enzymes during DNA replication, allowing each strand to serve as a template for synthesis of a new strand.

Describe what happens during DNA replication.

DNA replication is a semi-conservative process in which a team of enzymes, using each strand of the double helix as a template, synthesize new daughter strands. As a result, each DNA double helix consists of one strand from the parent molecule, and another strand that was synthesized anew (which is why the process is described as semi-conservative). Replication begins when an enzyme called helicase finds a sequence called the origin of replication. At the origin, helicase separates the double stranded DNA, exposing two single strands in a structure called a replication bubble. An enzyme called RNA primase lays down a short stretch of complementary RNA called a primer. The primer enables DNA polymerase to bind, and to use the template strand as a guide for synthesizing a complementary strand, always adding new nucleotides at the 3' end of a growing strand. In the leading strand, DNA replication is relatively continuous, as DNA polymerase follows the opening replication fork. In the lagging strand, DNA polymerase synthesizes new DNA in short sequences that are called Okazaki fragments. After DNA polymerase has laid down all of the complementary nucleotides that it can, an enzyme called ligase (with the help of other enzymes) removes the RNA primers, and seals a sugar-phosphate bond between DNA fragments. Throughout the process, enzymes called topoisomerases nick DNA's sugar phosphate backbone, preventing the DNA from overwinding, and then reseal the break.

Briefly describe the stages of mitosis.

During interphase, the cell grows and replicates its DNA. As a result, each chromosome consists of two identical sister chromatids. During prophase, the chromosomes condense as the nuclear membrane disintegrates. During metaphase, spindle fibers, generated from a centrosome, pull each chromosome to the cell equator. During anaphase, the sister chromatids are pulled apart, and dragged to opposite ends of the cell. During telophase, a new nuclear membrane forms around each set of chromosomes. Cytokinesis divides the cell into two daughter cells, each with a full (and identical) array of chromosomes, and a full set of cellular organelles

What is nondisjunction? What are its consequences? List some examples of conditions in humans caused by nondisjunction.

During meiosis there are two cell divisions. In each one, chromosomes get pulled apart. Meiosis I involves separation of homologous pairs of chromosomes. Meiosis II involves separation of sister chromatids. Nondisjunction means "failing to separate." A nondisjunction during meiosis I occurs when homologous pairs fail to separate. A nondisjunction during meiosis II means the sister chromatids fail to separate. The result is a gamete (sex cell) that either has an extra chromosome or a missing chromosome. If these gametes fuse with other gametes during fertilization, the result can be a zygote with an abnormal number of chromosomes. This can make the zygote unviable, or, as this zygote develops into a multicellular organism, developmental problems can arise. In humans, examples of conditions associated with nondisjunction include Turner Syndrome (females lacking an X chromosome), Klinefelter syndrome (males with an extra X chromosome), or Down Syndrome / trisomy 21.

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.

On a big picture level, explain how meiosis differs from mitosis.

Eukaryotic organisms contain two sets of chromosome, one from the mother, and one from the father. A cell with two sets of chromosomes is said to be diploid. During mitosis, the entire diploid set of chromosomes (which contains the entire genome) is duplicated and passed onto the daughter cells. Meiosis is a specialized form of cell division that is used by sexually reproducing organisms to create their sex cells, or gametes (sperm cells or eggs). When gametes are created during meiosis, the diploid set of chromosomes is reduced to a single set of chromosomes. A cell with a single set of chromosomes is said to be haploid. Whereas chromosomes created by mitosis are duplicated clones of the chromosomes in the parent cell, that's not true of the chromosomes created by meiosis. Because of a process called "crossing over," the chromosomes created by meiosis are novel, never-before-seen sequences of DNA. In addition, because of a process called independent assortment, the chromosomes passed from one parent to its offspring are unique combinations of the maternal and paternal chromosomes that an individual inherits from his or her parents. To summarize, mitosis clones the entire genome; meiosis reduces the genome from diploid to haploid, and creates genetic novelty in the process.

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 is electrophoresis, and how is it used to create DNA fingerprints (also known as DNA profiles)?

Gel electrophoresis involves placing molecules in a porous gel. Running an electrical current through the gel will cause the molecules placed in the gel to be sorted by size and electrical charge. This technique works particularly well with nucleic acids like DNA and RNA. That's because the phosphate groups in these molecules' sugar-phosphate backbone are negatively charged. This will move the molecules away from the negatively charged side of an electrophoresis chamber, and toward the positive side. At the same time, small fragments will be less impeded by the gel than large fragments, meaning that during the same period of time, smaller fragments will move more than larger ones, enabling the fragments to be sorted by size. Electrophoresis can be used to create "DNA fingerprints," unique patterns that can be traced to a specific individual. An early method of doing this involved restriction fragments. Because the DNA of any two individuals (who are not identical twins) is slightly different, applying the same restriction enzymes to different people's DNA will result in some differences in the restriction fragments that result. That's because restriction enzymes recognize specific sequences before making cuts in the DNA. Since sequences differ, some of the restriction sites in one individual's DNA won't be present in another person's DNA. Subsequent electrophoresis (which sorts these fragments by size), followed by using probes that enable visualization of a small percentage of the fragments, creates a unique pattern. More modern approaches to DNA profiling are based on repeated DNA sequences — variable number tandem repeats (VNTRs) or short tandem repeats (STRs) — found in humans and other eukaryotes. Because these repeated stretches of DNA vary in size from one individual to the next, they can be used to create a unique pattern for every individual. This technique is the basis of the CODIS (Combined DNA Index System) database used by the FBI and other law enforcement agencies.

Explain how viral life cycles can generate genetic and phenotypic diversity within their own viral populations.

Genetic and phenotypic diversity within viral populations can arise in two ways. The first is mutation that occurs during viral replication. The rate of mutation in DNA viruses is similar to that of eukaryotic cells. However, the mutation rate in RNA viruses can be significantly higher. The second is mixing of viral genomes. When two viruses invade the same host cell, the resulting viral offspring can wind up with recombined DNA from the two invading viruses. This type of recombination in influenza virus, which can infect humans, birds, and pigs, explains that virus's variability from year to year (and the consequent need for development of a new influenza vaccine each year).

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.

Describe the genetics and underlying biology of hemophilia.

Hemophilia is caused by a mutation in a clotting factor gene. These genes code for proteins that are part of the clotting cascade that happens whenever a person gets a cut or an internal injury. The most common mutations are in the genes for the proteins called "clotting factor 8" or "clotting factor 9." Hemophilia is a sex-linked, recessive condition. Because it's sex linked and recessive, a hemophiliac male can only pass the allele on to his daughters. Daughters can be homozygous normal, heterozygous, or homozygous recessive (which is the only way a female can be a hemophiliac). A heterozygous mother is known as a carrier, and she has a 50% chance of passing the allele on to her son's, who, if he inherits the allele, will express it. The disease has been a target of gene therapy clinical trials.

Explain what a monohybrid cross is, and what the results of such a cross will be. In your response, define the terms dominant and recessive.

If an individual possesses a dominant allele, she or he will express the phenotype that this allele codes for. Recessive alleles will only be expressed in individuals who are homozygous (and have inherited two copies of that allele). A monohybrid cross is a cross between two heterozygotes, such as cross between parents whose genotypes are Bb and Bb. The result of such a cross is offspring in a 3:1 ratio, with three individuals with the dominant phenotype to every one with the recessive phenotype. 1/4 of the offspring will be homozygous dominant, 2/4 will be heterozygous (and still have the dominant phenotype) and 1/4 will be homozygous recessive (and show the recessive phenotype).

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.

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).

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.

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.

Contrast "horizontal gene transfer" with "vertical gene transfer," and list and describe how horizontal gene transfer can occur in prokaryotes and eukaryotes.

In vertical gene transfer, parents transmit all or half of their genome to their offspring (depending on whether reproduction is asexual or sexual, respectively). In horizontal gene transfer, one organism transfers genes to another organism that is not its offspring. If the recipient is unicellular, then these newly acquired genes become part of the recipient's genome, and will then get passed to its offspring. In a multicellular organism, horizontal transfer only has long-lasting results if the genes are transferred into the germ line (the cells that create egg or sperm cells). An example is bacterial conjugation. Bacteria have, in addition to their main chromosome, small circles of DNA called plasmids. These plasmids can be copied in one bacterial cell, with the copy transmitted to a second bacterial cell via a membrane extension called a pilus. This transfer of plasmids transfers whatever genes are encoded on the plasmid to the second cell, which can, in turn, transmit this plasmid to another bacterial cell (or its offspring). Another example is transformation. In transformation, bacteria pick up DNA fragments from the environment, which become incorporated in the genome. Transformation and conjugation are largely limited to prokaryotes. Horizontal gene transfer that involves eukaryotes (as well as prokaryotes) can occur through viruses. During viral infections, the virus breaks apart the host's genome. Sometimes, DNA fragments from the host are mistakenly incorporated into a virus. As a result, when that virus infects a cell in another organism, it can bring in that other organism's DNA. If the virus infects a germ-line cell, then new genes can be incorporated into the gene pool of the recipient. This mechanism is called transduction. Finally, genes can be transferred horizontally between host cells and endosymbionts, such as mitochondria or chloroplasts. Over the course of eukaryotic evolution, mitochondria and chloroplasts have transferred up to 99% of their genes to their host cells (with these genes being incorporated into the genome of the host species). Since both mitochondria and chloroplasts are of bacterial origin, this amounts to a significant horizontal transfer of genetic material from bacteria to eukaryotes.

Explain how insulin and glucagon work to maintain blood glucose homeostasis.

Insulin and glucagon are hormones that are both produced in the pancreas, and they work together (but antagonistically) to maintain blood glucose homeostasis by keeping blood glucose levels near an optimal set point. When blood glucose levels increase above an optimal set point (which happens after a carbohydrate-rich meal), receptors on certain cells in the pancreas detect this higher level, and cause cells to respond by secreting insulin into the bloodstream. When insulin binds with insulin receptors in target tissues in the liver and skeletal muscles, these cells open up glucose channels. Glucose then diffuses from the blood into these cells, where it's converted into glycogen, a polysaccharide. In other tissues, the absorbed glucose is converted into fat. This activity lowers blood glucose levels back to the set point, and this feeds back to the pancreas, shutting down insulin secretion. When blood glucose levels fall (hours after eating), a second set of cells in the pancreas detect this drop, and, in response, secrete glucagon. Glucagon diffuses into the bloodstream. When glucagon binds with receptors in its target cells in the liver and skeletal muscles, it causes these cells to break down glycogen into glucose. The glucose diffuses into the bloodstream, raising blood glucose levels back to the set point. This is detected by cells in the pancreas, which shut down glucagon secretion.

What are linked genes? Describe their inheritance pattern, and explain which Mendelian rule linked genes don't follow.

Linked genes are genes on the same chromosome. Because they're on the same chromosome, they don't independently assort. Imagine a test cross involving two linked sets of genes: AaBb x aabb. If the genes weren't linked, you'd expect a 1:1:1:1 ratio of phenotypes in the offspring (Dominant-dominant; Dominant Recessive; Recessive-Dominant; recessive-recessive). But linked genes won't show this 1:1:1:1 ratio. The offspring will most commonly have one of the parental phenotypes, with a smaller percentage having recombinant phenotypes. If the linked alleles are far apart on the chromosome, the percentage of recombinants will approach 50% (making the results almost indistinguishable form independent assortment). But genes that are closely linked (physically close to one another on the chromosome) will rarely recombine. This percentage of recombination can be used to calculate the map distance between two alleles (also known as a centiMorgan).

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).

Describe what happens during meiosis I and meiosis II.

Meiosis I begins just as mitosis does: with an interphase that results in duplication of the chromosomes. During prophase 1, the chromosomes condense (as they do during mitosis). However, prophase I of meiosis also involves a process called synapsis, during which homologous chromosomes (the informationally matched chromosomes inherited from the mother and father) line up and exchange bits of DNA in a process called crossing over. This creates novel, never-before-seen sequences of DNA. During metaphase 1, homologous pairs, bound to one another through links called chiasma, are moved by the spindle to the cell equator. However, because each homologous pair is independent of every other, the orientation of the homologous pairs is different, setting the stage for the reassortment (or "mixing up") of chromosomes that were originally of maternal and paternal origins. During anaphase 1 the homologous pairs are pulled apart and dragged to opposing ends of the cell. What happens next varies by species: a telophase (in which the chromosomes spread out and a nuclear membrane reforms) might or might not occur. But all meiotic cells undergo cytokinesis I, creating two daughter cells which are haploid (possessing only one set of chromosomes), but with doubled chromosomes (consisting of two sister chromatids). During prophase II, spindle fibers attach to these doubled chromosomes, and pull them to the middle of the cell. They arrive in the middle during metaphase II. During anaphase II, sister chromatids are pulled apart. Telophase II follows, rebuilding the nucleus. Finally, cytokinesis II results in four haploid cells. Each cell has chromosomes with unique, never-before-seen DNA, and with a unique mixture of maternal and paternally derived chromosomes. In males, the result of meiosis is four sperm cells. In females, often three of the cells resulting from meiosis are sacrificed so that one one large egg cell results,

Explain the two ways by which meiosis creates genetic diversity.

Meiosis creates genetic diversity in two ways. First, during prophase I, homologous chromosomes pair up and exchange bits of DNA. This creates chromosomes with novel DNA sequences. These sequences are different from the corresponding sequences in the parents, and different from sibling to sibling. Second, because of independent assortment of maternal and paternal chromosomes during metaphase I, meiosis creates new chromosomal combinations, mixtures of chromosomes of maternal and paternal origin, different in each sibling. The possible number of differences resulting from independent assortment can be quantified as two to the number of homologous pairs. In other words, a species with 4 homologous pairs can create two to the fourth power (24) chromosomally distinct gametes (which equals 16). Humans, with 23 homologous pairs, can create 223 combinations of maternal and paternal chromosomes, which amounts to over 8 million chromosomally distinct gametes.

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.

Explain Mendel's principle of independent assortment.

Mendel discerned that gene pairs (for example, genes controlling height and those controlling flower color in garden peas) assort independently from one other. What that means is that the way that the alleles for, in this case, height are passed on to the offspring is independent of the way that the alleles for flower color are passed on to the offspring. Consider the dihybrid cross just mentioned above, represented by TtGg and TtGg. If these genes are assorting independently, then the result of this cross is going to be the combined result of independent crosses between Tt and Tt; and that between Gg and Gg. In each of these monohybrid crosses, the ratio of dominant to recessive offspring is 3:1. Because these alleles are passed on independently, you use the rule of multiplication to see the combined results. In other words, the result of the dihybrid cross is two traits with a 3 dominant:1 recessive ratio, multiplied by each other. Consequently, in the dihybrid cross the results will be 9:3:3:1, with 9/16 of the offspring showing both dominant traits, 3/16 showing one dominant and one recessive trait, 3/16 showing the other dominant and other recessive trait, and 1/16 showing both recessive traits.

What's the connection between Mendel's laws of inheritance and what happens during meiosis?

Mendel's first law is the principle of segregation. According to this principle, parents possess two alleles for each trait, but pass only one on to their offspring, which inherit their two alleles from their parents. This principle corresponds to the fact that sexually reproducing organisms have a diploid phase that produces haploid gametes. The diploid phase corresponds to the two alleles in each parent. The haploid phase corresponds to the one allele that each parent passes on to their offspring. In the zygote, the diploid condition is restored. Mendel's second law is the law of independent assortment: what happens to one gene pair is independent of every other gene pair (at least the ones that Mendel studied). Independent assortment of genes corresponds to the independent assortment of chromosomes that happens during metaphase 1 of meiosis.

What is non-nuclear inheritance?

Mitochondria and chloroplasts also have genetic material. In general, these organelles are only passed on to offspring through the female gamete, and thus don't follow Mendelian inheritance patterns. In the case of mitochondrial inheritance in animals, the male parent will not pass any of his mitochondria to his offspring. Rather, all of one's mitochondria are inherited from one's mother.

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.

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.

In relationship to the events of meiosis, explain how nondisjunction occurs.

Nondisjunction can occur during two phases during meiosis. The first is prophase 1 of meiosis 1. During that phase, homologous chromosomes come together and exchange pieces of DNA in a process that's called synapsis. Afterwards, these homologous pairs are moved to the cell equator by spindle fibers, and then pulled apart during anaphase 1. If the homologues fail to separate, then one of the resulting daughter cells will have an extra chromosome, and the other will be missing one. After meiosis II, when sister chromatids are pulled apart, all of the resulting gametes will either have an extra chromosome or a missing chromosomes. A second way that nondisjunction can happen is during meiosis II. In metaphase II, sister chromatids are moved, by the spindle, to the cell equator, and then pulled apart (during anaphase II). If sister chromatids fail to separate, then one of the resulting gametes will have an extra chromosome, while one will be missing a chromosome. In this case (nondisjunction during meiosis II), two the the four gametes will be normal, one will be missing a chromosome, and one will have an extra chromosome. These two ways are not mutually exclusive. If they occur together, the result can be gametes with two or three extra chromosomes, a duplication that's usually only survivable in X chromosomes.

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 two examples of induction during development.

One example of induction during development involves the dorsal lip of the blastopore inducing gastrulation in newts (a type of amphibian). This bit of tissue on a blastula (the hollow ball of cells that emerges early in development) releases morphogens that cause the blastula to develop into a three layered embryo (a gastrula). This was established by transplantation experiments carried out during the 1930s. If the dorsal lip of the blastopore from one newt embryo is transplanted onto another newt embryo, the transplanted tissue induces an entire second round of gastrulation. The result would be a kind of conjoined twin newt: two heads, two spinal cords, etc. A second example of induction is the zone of polarizing activity (ZPA) inducing limb formation in vertebrate forelimbs. The embryonic limb bud in a vertebrate has a patch of inducing cells called the zone of polarizing activity, or ZPA. The ZPA secretes a morphogen called sonic hedgehog (abbreviated as "Shh"). Shh diffuses from the ZPA, so that the tissue nearest to it receives the highest dose of this morphogen, while the tissue furthest away receives the weakest dose. The result (in humans) is a pinky finger developing from the tissue that receives the highest dose of morphogen, a thumb developing in the tissue that receives the lowest dose of morphogen, with other tissues developing into the fingers in between.

Using RNA interference as an example, describe the role of small RNA molecules in regulating gene expression.

One of the main functions of small RNA molecules (typically about 22 nucleotides long) is RNA interference. In RNA interference, small RNAs bind with messenger RNA, often blocking translation of the mRNA into protein, and sometimes signaling for that mRNA's enzymatic destruction.

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 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.

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.

What are polygenic traits, and what is their inheritance pattern?

Polygenic traits are traits that are controlled by more than one gene. Examples in humans include the genes that control for the inheritance of height and skin color. In maize, kernel color is also controlled by at least three genes. Traits that are under the control of multiple genes do not show a binary distribution, as do traits controlled by a single genes (think of cystic fibrosis: you either have it, or you don't). Rather, traits under the control of multiple genes tend to have what's called a normal distribution, with an array of phenotypes. Using height as an example, most individuals are of average height: some individuals are very tall, and others are very short, with heights arrayed along a bell shaped curve.

What is polyploidy?

Polyploidy is a doubling (or more) of chromosome number. If it occurs in a gamete which is subsequently fertilized, and if that zygote is viable, it can lead to a form of sympatric speciation that occurs, essentially, within one generation. The same can occur if polyploidy occurs during mitosis, followed by vegetative propagation (a form of asexual reproduction that occurs in plants like strawberries or aspen trees). Polyploidy is rare in animals, but seems to be a common mechanism for speciation in plants. It's estimated that between 30% to 80% of plant species arose through some type of polyploidy resulting in duplication of entire sets of chromosomes.

What is a frameshift mutation?

Protein coding genes have a reading frame. That's because codons are sequences of 3 RNA bases, and starting with the start codon on a stretch of mRNA, the codons are read one at a time, with each codon being converted into an amino acid. A frameshift mutation involves the insertion or deletion of a nucleotide in DNA in a way that disrupts the reading frame in mRNA, causing all of the codons following the mutation to be misread by the ribosome. The most common result of this is extensive missense (codons coding for the wrong amino acid), though nonsense and silent mutations (coding for a stop codon) are also possible.

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.

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.

What are sex linked genes? Explain their inheritance pattern.

Sex linked genes are genes that are located on the X chromosome. As a result, males can't be heterozygous. They either have a sex linked allele, or they don't. Males who have a sex linked allele will pass it on to their daughters. If the allele is recessive, then female heterozygotes will be carriers, possessing the allele, but not expressing the associated phenotype. However, female heterozygotes have a 1 in 2 probability of passing the allele on to their male offspring. A male with a sex linked allele cannot pass it on to his son, but he will pass the allele on to his daughter. For a female to express the phenotype of a recessive sex linked trait, her mother has to be a carrier, and her father has to possess the allele (and thus the associated condition).

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.

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 the overall flow of genetic information of cells.

The basic flow of information in cells is from DNA, which is transcribed into RNA, which is translated into protein. More specifically, information flows from a sequence DNA triplets to mRNA codons to amino acids.

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.

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.

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.

What is the rule of multiplication, and when do you use it?

The rule of multiplication is the idea that the probability of independent events occurring together is the product of their individual probabilities. Let's say you were asked to determine the probability of genotype aabbcc resulting from a trihybrid cross (AaBbCc x AaBbCc). Solving this with a Punnett square would be a nightmare: the square would be a table with 64 cells. Instead, use the rule of probability. The chance of Aa x Aa producing aa is 1/4. The chance of Bb x Bb producing bb is also 1/4, and that's also the probability of an offspring having the genotype cc. Because these alleles assort independently, you can use the rule of multiplication: 1/4 x 1/4 x 1/4 = 1/64.

List the six key elements in living things.

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

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.

Explain how human genes can be transferred to bacterial cells that subsequently produce human gene products (such as insulin). Your answer should include 1) dealing with introns, 2) creating a recombinant DNA vector, and 3) inserting the recombinant DNA into a suitable host.

Transfer of protein coding genes between any two organisms is possible because all organisms share the same genetic code: a deep homology that underlies all of life. However, transferring protein coding genes from eukaryotes to prokaryotes is made difficult because of the presence of introns within eukaryotic genes. Introns are non-coding sequences that have to be spliced out before the gene's RNA can be translated into protein. So, to transfer a human gene to a bacterium in order to create a gene product, you have to start with intron-free DNA. That can be acquired by finding cells that produce the desired protein, extracting the relevant mRNA from those cells, and using reverse transcriptase to create cDNA (complementary DNA) from the mRNA. Or, if you know the amino acid sequence for the protein, you can reverse-engineer DNA that codes for that amino acid sequence. Once that's been done, the DNA needs to be cut with a restriction enzyme so that its ends are sticky: that means that they have single stranded overhangs ready to form hydrogen bonds with complementary sequences. Restriction endonucleases are enzymes originally of bacterial origin, and finding specific sequences and making sticky ended cuts is exactly what they do. The next step is to extract a plasmid - a small circle of extrachromosomal DNA - from a bacterial cell, and then to cut open that plasmid with the same restriction endonuclease used to cut the sticky ends on the human DNA. If the human DNA fragment and the plasmid DNA are combined, they'll combine by forming hydrogen bonds between their complementary sticky ends. The next step is to add another enzyme, DNA ligase. DNA ligase creates sugar phosphate bonds between adjacent, unbonded nucleotides. The result is a recombinant plasmid: one that contains its own DNA, plus human DNA. This plasmid can be inserted into a bacterial cell through the technique of transformation. And once inside a bacterial cells, that bacterial cell can be cultured, and the desired protein purified and otherwise made ready for use.

Describe how trisomy 21/Down syndrome occurs.

Trisomy 21/Down Syndrome is a developmental condition that results in lowered intellect, short stature, and a recognizable facial phenotype involving a round face and almond shaped, upward slanting eyes. The cause is nondisjunction of the 21st chromosome during meiosis, generally in the egg. As a result, the egg (or, less frequently, the sperm) carries two copies of chromosome 21 instead of one, and after fertilization, the zygote has three copies of chromosome 21, instead of a homologous pair. The reason why eggs are suspected as the source of the nondisjunction is the positive correlation between maternal age and Down syndrome: it's thought that older eggs (eggs cells are as old as the mother) are more prone to nondisjunction than younger eggs. At the same time, because birth by young women is so much more common, the majority of Down Syndrome children are born to women under 35 years old.

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).

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.

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.

List the three principal forms of RNA, and describe the function of each one.

mRNA is messenger RNA. It's job is to bring instructions from the DNA to ribosomes, where those instructions can be translated into protein. mRNA's information is encoded in 3 base sequences called codons, each of which codes for an amino acid, a start codon, or a stop codon. tRNA is transfer RNA. During protein synthesis, tRNAs brings specific amino acids to ribosomes, allowing the ribosomes to bind amino acids together into polypeptides, following the sequence laid down by mRNA. tRNAs have a region called an "anticodon." The anticodon is composed of three RNA nucleotides, and it complements (and binds with) codons on mRNA, which is the basis of the information transfer between RNA and protein. rRNA is ribosomal RNA. Along with protein, rRNA makes up ribosomes. In fact, the catalytic part of the ribosome is composed of rRNA.