LIFESCI 7A Learning Life Objectives

Describe the structure of an atom

An atom consists of a nucleus containing positively charged protons and neutral neutrons, surrounded by negatively charged electrons in orbitals. The number of protons determines the element. Electrons determine how atoms interact and form bonds.

Explain how nonpolar and polar covalent bonds are formed between atoms.

Covalent bonds form when atoms share electrons. In a nonpolar covalent bond, electrons are shared approximately equally. In a polar covalent bond, electrons are shared unequally because one atom has greater electronegativity, producing partial charges (δ⁺ and δ⁻).

Explain how the potential energy of two atoms changes as they form or break a bond.

As atoms approach and form a stable bond, their potential energy decreases and energy is released. Breaking the bond requires energy to overcome the attractive interactions. A stable bond forms at the distance where potential energy is minimized.

Describe each type of chemical bond and intermolecular force: nonpolar covalent bonds, polar covalent bonds, ionic bonds, hydrogen bonds, and van der Waals' forces.

• Nonpolar covalent: Atoms share electrons approximately equally.

• Polar covalent: Atoms share electrons unequally, producing partial charges.

• Ionic: Electrostatic attraction between oppositely charged ions formed when electrons are transferred or redistributed.

• Hydrogen bond: Attraction between a partially positive hydrogen bonded to an electronegative atom (usually O or N in biology) and another electronegative atom.

• Van der Waals forces: Weak attractions caused by temporary or induced dipoles between nearby atoms or molecules.

Define and relate the terms electronegativity, polarity, hydrophilic, and hydrophobic.

• Electronegativity: An atom's ability to attract shared electrons.

• Polarity: Unequal distribution of electrical charge in a bond or molecule.

• Hydrophilic: Water-attracting; typically polar or charged and able to interact favorably with water.

• Hydrophobic: Water-avoiding; typically nonpolar and unable to form favorable interactions with water.

Greater electronegativity differences generally create more polar bonds. Polar and charged substances tend to be hydrophilic, while nonpolar substances tend to be hydrophobic.

Identify the number of covalent bonds formed by H, C, O, and N.

• Hydrogen (H): 1 bond

• Carbon (C): 4 bonds

• Oxygen (O): 2 bonds

• Nitrogen (N): usually 3 bonds

Compare and contrast the relative electronegativities of H, C, O, and N.

From highest to lowest: O comparable to N, C comparable to H. Oxygen attracts shared electrons most strongly, followed by nitrogen, carbon, and hydrogen. Hydrogen and Carbon are usually low electronegativity, meanwhile Oxygen and Nitrogen are considered high.

Determine whether a region of a molecule is likely to be polar or nonpolar based on its chemical structure and the relative electronegativity of its atoms.

Look for polar bonds and the molecule's shape. Bonds involving O or N are often polar. If bond dipoles cancel because of molecular symmetry, the overall region may be nonpolar. Hydrocarbon regions consisting mainly of C–C and C–H bonds are generally nonpolar.

Relate the potential energy change of an atomic interaction to its "strength".

A stronger attractive interaction generally corresponds to a deeper potential-energy minimum. More energy is needed to separate the interacting particles. A weaker attraction has a shallower minimum and requires less energy to overcome.

Compare the relative strengths of bonds and electrostatic interactions and relate these strengths to the amount of energy required to break them.

Covalent bonds are generally strong chemical bonds. Ionic attractions can be strong between isolated ions, but their effective strength depends on the environment. Hydrogen bonds are weaker than covalent bonds, and individual van der Waals interactions are usually weaker still. In water, ionic interactions are weakened by water's polarity. Breaking an interaction requires energy; forming one releases energy.

Determine whether a molecule is able to participate in hydrogen bonding with itself or another molecule based on its chemical structure and relative electronegativity of its atoms.

A molecule can donate a hydrogen bond when it has a hydrogen covalently bonded to an electronegative atom such as O or N. It can accept a hydrogen bond when it has an appropriate electronegative atom with an available lone pair. Water, alcohols, and molecules with N–H or O–H groups can often participate. A molecule can form hydrogen bonds with itself only if suitable donor and acceptor sites are present.

Determine whether a region of a molecule is likely to be hydrophilic or hydrophobic based on its ability to form hydrogen bonds with water.

Regions with charged groups or polar groups that can hydrogen-bond with water are generally hydrophilic. Regions dominated by nonpolar C–C and C–H bonds are generally hydrophobic because they cannot form comparable favorable interactions with water.

Determine whether a given molecule could exist in nature, based on your knowledge of the number of electrons each element can share.

Check whether its atoms have plausible valences and satisfy typical bonding rules: H usually forms 1 bond, O 2, N 3, and C 4. Structures that give atoms unreasonable numbers of bonds or violate charge and valence rules are generally implausible. Some exceptions occur with ions, radicals, and elements that can have expanded valence shells.

Differentiate between hydrogen bonds, covalent bonds, ionic bonds, and Van der Waals interactions.

Covalent bonds involve sharing electrons within molecules. Ionic interactions are attractions between charges. Hydrogen bonds are directional attractions involving a partially positive hydrogen and an electronegative atom. Van der Waals interactions arise from temporary or induced charge distributions. Covalent bonds usually hold atoms together within molecules, while the other three commonly contribute to interactions between molecules or molecular regions.

Compare and contrast the organization of prokaryotic/eukaryotic cells and plant/animal cells.

• Prokaryotic cells: Lack a membrane-bound nucleus and membrane-bound organelles. Their DNA is in a nucleoid region. Examples include bacteria and archaea.

• Eukaryotic cells: Have a nucleus and membrane-bound organelles. Examples include plants, animals, fungi, and protists.

• Plant cells: Have a cellulose cell wall, chloroplasts in photosynthetic tissues, and typically a large central vacuole.

• Animal cells: Lack cell walls and chloroplasts and commonly have lysosomes and a flexible extracellular matrix.

Both plant and animal cells are eukaryotic and share structures such as the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, and plasma membrane.

Define the terms organelle, cytoplasm, and cytosol.

• Organelle: A specialized cellular structure that performs a particular function.

• Cytosol: The fluid portion inside the cell, excluding organelles and other structures.

• Cytoplasm: Everything between the plasma membrane and the nucleus in a eukaryotic cell, including cytosol and organelles.

Describe the function of common eukaryotic organelles: mitochondria, chloroplast, nucleus, endoplasmic reticulum, Golgi apparatus, lysosome, and vacuole.

• Mitochondria: Produce most ATP during aerobic cellular respiration.

• Chloroplasts: Carry out photosynthesis in plants and algae.

• Nucleus: Contains most cellular DNA and regulates gene expression.

• Endoplasmic reticulum (ER): Rough ER synthesizes and processes proteins destined for secretion or membranes; smooth ER synthesizes lipids and participates in detoxification and calcium storage.

• Golgi apparatus: Modifies, sorts, and packages proteins and lipids for delivery.

• Lysosomes: Use digestive enzymes to break down macromolecules, damaged components, and cellular waste.

• Vacuoles: Store water and substances; plant central vacuoles also maintain turgor pressure and help with waste storage.

Identify the structures of different lipids: triglycerides, fatty acids, phospholipids, and cholesterol.

• Triglyceride: One glycerol molecule bonded to three fatty acids; primarily used for energy storage.

• Fatty acid: A hydrocarbon chain with a terminal carboxyl group.

• Phospholipid: Usually a glycerol backbone, two fatty acid tails, and a phosphate-containing polar head group; forms the basis of cell membranes.

• Cholesterol: A lipid with four fused carbon rings, a small hydroxyl group, and a hydrocarbon tail; helps regulate animal cell membrane fluidity.

Differentiate between saturated and unsaturated fatty acids.

• Saturated fatty acids: Have no carbon–carbon double bonds; their chains are relatively straight and pack closely together.

• Unsaturated fatty acids: Have one or more carbon–carbon double bonds. Cis double bonds introduce bends that prevent close packing.

Saturated tails generally make membranes less fluid; cis-unsaturated tails generally make them more fluid.

Describe the structure of the plasma membrane and the different ways that proteins can be associated with the lipid bilayer.

The plasma membrane is a phospholipid bilayer with hydrophilic heads facing the watery environments and hydrophobic tails facing inward. It contains proteins, cholesterol in animal cells, and carbohydrate groups.

• Integral proteins: Embedded in the bilayer; some span the entire membrane.

• Peripheral proteins: Attached to the membrane surface or to other membrane proteins.

• Lipid-anchored proteins: Covalently attached to lipid molecules embedded in the membrane.

The membrane regulates transport, communication, recognition, and interactions with the environment.

Predict the primary function of a cell based on the molecules and organelles it contains.

Cells contain structures suited to their jobs. Many mitochondria suggest high energy demand. Abundant rough ER and Golgi suggest protein production and secretion. Extensive smooth ER suggests lipid synthesis or detoxification. Many chloroplasts indicate photosynthesis. Numerous lysosomes suggest extensive intracellular digestion.

Predict the relative abundance of organelles in different cells based on their functions.

Cells have more of the organelles required for their functions. Muscle cells generally have many mitochondria; protein-secreting cells have abundant rough ER and Golgi; steroid-producing cells have abundant smooth ER; photosynthetic leaf cells contain many chloroplasts. Not every cell has the same organelle composition.

Discuss how visual representations (models) of biological systems can be both useful and misleading.

Models simplify complex systems so we can see structures, relationships, and processes more clearly. However, they may distort scale, omit components, freeze dynamic processes, or exaggerate certain features. A model is useful for answering particular questions but is not a perfect copy of reality.

Predict the structure of a phospholipid membrane in hydrophilic vs. hydrophobic environments.

• In water: Phospholipids generally arrange into bilayers or micelles, with hydrophilic heads facing water and hydrophobic tails shielded from it.

• In a nonpolar, hydrophobic environment: The arrangement can reverse, with hydrophobic tails facing the nonpolar environment and hydrophilic heads shielded inside. The exact structure depends on the surrounding solvent and lipid geometry.

Evaluate how changing temperature, phospholipid chain length, and phospholipid saturation affects membrane fluidity.

• Higher temperature: Increases fluidity; lower temperature decreases it.

• Longer fatty acid tails: Decrease fluidity because they have more contact area and stronger van der Waals interactions.

• Shorter fatty acid tails: Increase fluidity.

• More cis-unsaturated tails: Increase fluidity because their bends prevent tight packing.

• More saturated tails: Decrease fluidity because straight chains pack closely.

Cholesterol buffers fluidity: it generally restrains phospholipid movement at high temperatures and prevents tight packing at low temperatures.

Explain how the chemical properties of a phospholipid bilayer allow it to act as a semipermeable membrane.

The bilayer's hydrophobic interior allows small nonpolar molecules, such as O₂ and CO₂, to pass relatively easily. It restricts most ions and large or polar molecules. Specific transport proteins allow selected substances to cross, making the membrane selectively permeable.

Define and relate the terms diffusion, tonicity, osmosis, hypertonic, hypotonic, and isotonic.

• Diffusion: Net movement of particles from higher to lower concentration due to random motion.

• Osmosis: Net movement of water across a selectively permeable membrane toward the side with higher effective solute concentration.

• Tonicity: The effect of a solution's nonpenetrating solutes on a cell's volume.

• Hypertonic solution: Has a higher effective solute concentration than the comparison solution; water tends to leave the cell.

• Hypotonic solution: Has a lower effective solute concentration; water tends to enter the cell.

• Isotonic solution: Has equal effective solute concentrations; there is no net water movement.

Water still moves in both directions in an isotonic environment, but the rates are equal.

Compare and contrast the different passive (simple diffusion, facilitated diffusion) and active (primary, secondary) transport mechanisms.

• Simple diffusion: Passive movement directly through the lipid bilayer, down a concentration gradient.

• Facilitated diffusion: Passive movement down an electrochemical gradient through a channel or carrier protein.

• Primary active transport: Uses energy directly, often from ATP hydrolysis, to move substances against their electrochemical gradients.

• Secondary active transport: Uses energy stored in an ion gradient, usually created by primary active transport, to drive another substance against its gradient. Symport moves substances in the same direction; antiport moves them in opposite directions.

Passive transport does not require direct energy input to move a substance down its gradient. Active transport can move a substance against its gradient.

Predict the permeability of a molecule based on its chemical properties.

Small nonpolar molecules cross most easily. Small uncharged polar molecules cross more slowly. Large polar molecules cross poorly without transport proteins. Ions cross the hydrophobic bilayer extremely poorly without channels or transporters. Charged and polar molecules generally require membrane proteins.

Predict the net movement of water based on the relative tonicity of two solutions.

• Cell in a hypertonic solution: Water leaves; the cell shrinks.

• Cell in a hypotonic solution: Water enters; the cell swells and may burst if it lacks sufficient structural support.

• Cell in an isotonic solution: No net water movement; cell volume stays approximately constant.

In plants, a hypotonic environment promotes turgor pressure, while a hypertonic environment can cause plasmolysis.

Predict the rate and direction of net movement of molecules based on their concentration gradients and the absence or presence of specific membrane transport proteins.

Net passive movement follows the concentration gradient for uncharged solutes, or the electrochemical gradient for ions, from higher to lower electrochemical potential. A steeper gradient generally increases the rate of diffusion. Channels and carriers can increase transport rates and selectivity. Without a suitable transport protein, an impermeable substance crosses very slowly. Active transport can move substances against their gradients using energy.

Define and differentiate the terms metabolism, anabolism, and catabolism.

• Metabolism: All chemical reactions occurring in an organism or cell.

• Anabolism: Builds complex molecules from simpler ones; requires energy overall.

• Catabolism: Breaks down complex molecules into simpler ones; often releases energy that can be captured in ATP or electron carriers.

Define the terms kinetic energy and potential energy.

• Kinetic energy: Energy of motion, such as moving molecules.

• Potential energy: Stored energy due to position, arrangement, or chemical structure, such as energy associated with chemical gradients and molecular interactions.

Explain the first and second laws of thermodynamics.

• First law: Energy cannot be created or destroyed, only transferred or transformed.

• Second law: Every spontaneous process increases the total entropy of an isolated system. Energy transformations disperse some energy, often as heat, reducing the amount available to do useful work.

Define and relate the terms free energy, enthalpy, entropy, exergonic, and endergonic.

• Free energy (G): Energy available to do useful work at constant temperature and pressure.

• Enthalpy (H): A measure of a system's heat content at constant pressure.

• Entropy (S): A measure related to energy dispersal and the number of possible microscopic arrangements.

• Exergonic reaction: Has negative free energy change (ΔG < 0); thermodynamically favorable.

• Endergonic reaction: Has positive free energy change (ΔG > 0); requires energy input to proceed.

The relationship is:

ΔG = ΔH - TΔS

Here, T is absolute temperature in kelvin. A reaction is thermodynamically favorable when ΔG is negative.

Discuss how an endergonic reaction can be “coupled” to an exergonic reaction.

An endergonic reaction can proceed when coupled to an exergonic reaction so that the sum of their free energy changes is negative. In cells, ATP hydrolysis is commonly coupled to energy-requiring reactions.

For example, ATP hydrolysis can provide the energy needed to synthesize a molecule that would not form spontaneously on its own.

Define and relate the terms substrate, active site, activation energy, transition state, and reaction rate.

• Substrate: The reactant on which an enzyme acts.

• Active site: The region of an enzyme where the substrate binds and the reaction occurs.

• Activation energy (Ea): The energy barrier that must be overcome for a reaction to proceed.

• Transition state: A high-energy, unstable arrangement of atoms during the conversion of reactants into products.

• Reaction rate: How quickly reactants are converted into products.

Describe in general terms how enzymes are able to alter the rate of chemical reactions.

Enzymes are biological catalysts that lower activation energy by stabilizing the transition state and providing a favorable reaction environment. They increase reaction rates without being consumed. They do not change the overall ΔG of a reaction or its equilibrium position.

Explain how small molecules (e.g., drugs or regulatory molecules) are able to increase or decrease the activity of an enzyme.

• Activators: Increase enzyme activity by stabilizing an active form or improving substrate binding.

• Inhibitors: Decrease activity by blocking substrate binding or altering enzyme function.

• Competitive inhibitors: Compete with the substrate for the active site; their effects can often be overcome by increasing substrate concentration.

• Noncompetitive inhibitors: In the pure noncompetitive case, bind at another site and reduce catalytic activity; increasing substrate concentration does not overcome the inhibition.

• Allosteric regulators: Bind at a site other than the active site and change enzyme activity.

Predict whether a reaction will be exergonic or endergonic based on ΔH and ΔS.

Use ΔG = ΔH - TΔS

ΔH	ΔS	Prediction
Negative	Positive	Exergonic at all temperatures
Positive	Negative	Endergonic at all temperatures
Negative	Negative	Favorable at low temperatures
Positive	Positive	Favorable at high temperatures

These predictions assume the signs of ΔH and ΔS remain approximately constant over the temperature range.

Determine whether two reactions can be successfully coupled based on their changes in free energy.

Add their free energy changes:

ΔG(total) = ΔG(1) + ΔG(2)

If the total is negative, the coupled process is thermodynamically favorable. If the total is positive, it is unfavorable under those conditions. A total of zero is at equilibrium. The reactions must be coupled through a suitable mechanism, not merely occur in the same cell.

Evaluate how changing cellular conditions will change the free energy of a reversible reaction.

For a reaction under cellular conditions:

• ΔG = ΔG°′ + RT ln(q)

• ΔG°′: Standard transformed free energy change at biochemical standard conditions.

• R: Gas constant.

• T: Absolute temperature.

• Q: Reaction quotient, calculated from current product and reactant concentrations.

Increasing product concentrations or decreasing reactant concentrations generally makes the forward reaction less favorable. Increasing reactant concentrations or removing products generally makes it more favorable. At equilibrium, ΔG = 0. Changing pH, temperature, or other conditions can also change ΔG.

Interpret graphs of free energy vs. progress of reaction to determine the thermodynamic favorability, likelihood of coupling, and relative rates of reactions for different chemical reactions.

• Products lower in free energy than reactants: ΔG is negative; the reaction is exergonic.

• Products higher in free energy than reactants: ΔG is positive; the reaction is endergonic.

• Products and reactants at the same free energy: ΔG = 0 under those conditions.

• Activation energy: The vertical difference between the reactants and the transition-state peak.

• Enzyme effect: Lowers the activation energy but does not change the free energy difference between reactants and products.

A reaction with a lower activation-energy barrier generally proceeds faster under comparable conditions. ΔG alone does not tell you the reaction rate.

Interpret data to assess changes in enzyme function and predict the effects (i.e., activating or inhibiting) of regulatory molecules.

Compare reaction rates under different conditions. An increased rate after adding a molecule suggests activation; a decreased rate suggests inhibition, assuming other variables are controlled. Changes in substrate concentration, enzyme concentration, temperature, and pH must be considered before attributing a rate change to a regulator.

Evaluate the effect of regulatory molecules (e.g., feedback inhibitors) on metabolic pathways.

In feedback inhibition, the final product of a pathway inhibits an enzyme acting earlier in that pathway, often the first committed step. When product accumulates, the pathway slows; when product levels fall, inhibition decreases and the pathway can resume. This prevents wasteful production and conserves energy and resources.

In feedback activation, the final product of a pathway activates an enzyme acting earlier in that pathway, often the first committed step. When product accumulates, the pathway increases; when product levels fall, activation decreases the pathway gets slower.

Relate the pH scale to the concentration of hydrogen ions (aka H+ or “protons”) in a solution.

pH = -log(base10) [H⁺]

• Lower pH means higher H⁺ concentration and greater acidity.

• Higher pH means lower H⁺ concentration and greater basicity.

• A change of one pH unit represents a tenfold change in H⁺ concentration.

For example, a solution at pH 5 has 10 times the H⁺ concentration of a solution at pH 6.

Evaluate environmental effects (e.g., pH, temperature) on enzyme catalyzed reactions rates.

Each enzyme has an optimal temperature and pH range. Increasing temperature usually increases reaction rate up to an optimum, but excessive heat can disrupt the enzyme's structure and cause denaturation. Temperatures below the optimum generally slow molecular motion. pH changes can alter the charges and shapes of amino acids, affecting substrate binding and catalysis. Extreme pH can denature an enzyme.

Relate anabolic and catabolic pathways to overall changes in free energy.

Catabolic pathways break down molecules and are often exergonic, capturing released energy in ATP and reduced electron carriers. Anabolic pathways build molecules and are often endergonic, requiring energy and reducing power. Cells frequently couple catabolism to anabolism so the overall process is thermodynamically favorable.

Interpret free energy diagrams to predict the free energy changes involved in a reaction, the kinetics of a reaction, and the impact of adding an enzyme to a reaction.

• Calculate ΔG by subtracting the reactants' free energy from the products' free energy.

• A negative ΔG indicates an exergonic reaction; a positive ΔG indicates an endergonic reaction.

• The activation-energy barrier determines how difficult it is for reactants to reach the transition state.

• A larger activation-energy barrier generally means a slower reaction under comparable conditions.

• Adding an enzyme lowers the activation-energy barrier but leaves ΔG unchanged.

• Coupling reactions can make the overall ΔG negative if their free energy changes sum to a negative value.

Interpret enzyme kinetics graphs to determine the relative rate of an enzyme catalyzed reaction under different reaction conditions.

• Reaction rate versus substrate concentration: The rate generally increases as substrate concentration rises, then approaches a maximum (Vmax) when the enzyme becomes saturated.

• Km: In the simple Michaelis–Menten model, the substrate concentration at half Vmax. A lower Km often indicates higher apparent substrate affinity, though this interpretation depends on the mechanism.

• Competitive inhibition: Increases apparent Km but leaves Vmax unchanged in the basic model.

• Pure noncompetitive inhibition: Decreases Vmax while leaving Km unchanged.

• Uncompetitive inhibition: Decreases both apparent Km and Vmax.

• Enzyme activation: Can increase reaction rate by improving catalytic activity or substrate binding.

• Enzyme inhibition: Can reduce reaction rate by blocking binding or catalysis.

To predict a drug's effect, compare enzyme activity with and without the drug under the same conditions. Consider substrate concentration, inhibitor type, and whether the drug changes the enzyme's catalytic capacity or its apparent substrate affinity.

Predict the impact of different drugs on enzyme activity based on varying reaction conditions.

Drugs affect enzyme activity by inhibiting or activating enzymes. Competitive inhibitors can be overcome by increasing substrate concentration; noncompetitive inhibitors lower V(max). Drug effects also depend on drug concentration, temperature, and pH.