Life Science 7A - Chemistry of Life (Week 1a)

What are the three main subatomic particles, and what are their charges and locations?

Protons: positive (+1), in the nucleus. Neutrons: no charge, in the nucleus. Electrons: negative (−1), in orbitals/electron clouds around the nucleus. Nearly all atomic mass is in the nucleus.

What determines an element's identity?

Its number of protons (atomic number). Changing the number of protons changes the element.

What are isotopes?

Atoms of the same element with the same number of protons but different numbers of neutrons. They have the same chemical identity but different masses.

What is a valence electron, and why does it matter in biology?

A valence electron is in an atom's outermost occupied shell. Valence electrons determine how atoms bond and react.

How many covalent bonds do H, C, N, and O usually form in stable biological molecules?

H usually forms 1 bond; C forms 4; N usually forms 3; O usually forms 2. These are useful patterns, not rules that cover every unusual chemical situation.

What does it mean for atoms to share electrons in a covalent bond?

Their electron clouds are shared between nuclei. Sharing helps atoms reach a more stable electron arrangement; the shared electrons attract both positively charged nuclei.

How does a nonpolar covalent bond differ from a polar covalent bond?

In a nonpolar covalent bond, electrons are shared about equally. In a polar covalent bond, one atom attracts the shared electrons more strongly, creating partial charges (δ− and δ+).

What is electronegativity?

An atom's tendency to attract shared electrons in a chemical bond. Oxygen and nitrogen are more electronegative than carbon and hydrogen.

Rank H, C, N, and O from lowest to highest electronegativity.

Approximate order: H < C < N < O. Oxygen attracts shared electrons most strongly among these four.

A C–H bond is shown in a molecular model. Is it strongly polar or mostly nonpolar, and why?

Mostly nonpolar: carbon and hydrogen have relatively similar electronegativities, so the electrons are shared fairly evenly.

A model shows an O–H bond. Which atom is partially negative, and why?

Oxygen is δ− and hydrogen is δ+, because oxygen attracts the shared electrons more strongly.

What makes an entire molecule polar? Is one polar bond enough?

A molecule has an uneven distribution of charge. Polar bonds contribute, but shape matters: bond dipoles can cancel in a symmetrical molecule, so one must consider the whole structure.

How can you use a structural model to decide whether a region of a molecule is polar?

Identify electronegative atoms such as O or N, inspect bonds such as O–H, N–H, C–O, and C–N, and consider whether the bond dipoles cancel because of the region's geometry. Hydrocarbon regions are usually nonpolar.

What is the difference between a partial charge and a full ionic charge?

Partial charges (δ+ and δ−) result from unequal sharing in a polar covalent bond. Full ionic charges result when atoms transfer electrons and become ions, such as Na+ and Cl−.

How does an ionic bond form?

Electron transfer creates oppositely charged ions, which attract electrostatically. In water, many ionic compounds dissociate into separate hydrated ions.

What is a hydrogen bond?

A relatively weak, directional attraction between a partially positive hydrogen covalently bonded to an electronegative atom (often O or N) and another electronegative atom with a lone pair.

What are van der Waals interactions?

Weak attractions that occur when electron distributions create temporary or induced dipoles. Individually weak, they can matter when many close contacts occur.

How do covalent bonds, ionic interactions, hydrogen bonds, and van der Waals interactions compare in typical biological contexts?

Covalent bonds are generally strongest and require the most energy to break. Ionic attractions can be strong in dry environments but are weakened by water. Hydrogen bonds are weaker individually. Van der Waals interactions are usually weakest individually. Context and geometry affect actual strengths.

What does a potential-energy curve for two atoms show?

At large separation, interaction energy approaches a baseline. As atoms approach, attraction lowers potential energy to a minimum at the preferred bond distance. If they get too close, repulsion makes energy rise steeply.

On a potential-energy graph, what does the bottom of the energy well represent?

The most stable separation (equilibrium bond length), where attractive and repulsive effects balance and potential energy is lowest.

How does bond strength relate to the depth of a potential-energy well?

A deeper well usually means more energy is needed to separate the atoms completely; the interaction is stronger.

Does breaking a covalent bond release energy or require energy?

Breaking a bond requires energy input. Forming a bond releases energy. Overall reaction energy depends on both bonds broken and bonds formed.

Why can an ionic interaction be weaker in water than in a nonpolar environment?

Water is polar and surrounds ions, shielding their charges and stabilizing them separately. This reduces the attraction between the ions.

What makes a molecule hydrophilic?

It interacts favorably with water, often because it has charged or polar regions that can form ion–dipole interactions or hydrogen bonds with water.

What makes a molecule hydrophobic?

It is largely nonpolar and cannot make favorable interactions with water. Nonpolar surfaces tend to cluster together in water, minimizing their contact with it.

How are polarity, hydrophilicity, and hydrophobicity related?

Polar or charged regions are often hydrophilic because they interact with water. Nonpolar hydrocarbon regions are usually hydrophobic. These are related tendencies, not absolute labels for every molecule.

Can a molecule with both polar and nonpolar regions exist? What is it called, and why does it matter?

Yes. It is amphipathic (amphiphilic). For example, a phospholipid has a hydrophilic head and hydrophobic tails, allowing it to form bilayers in water.

What features are needed for a molecule to donate a hydrogen bond?

Typically, a hydrogen covalently bonded to O or N (such as an O–H or N–H group). A C–H bond is generally not a strong hydrogen-bond donor in introductory biology.

What features are needed for a molecule to accept a hydrogen bond?

An electronegative atom, usually O or N, with an available lone pair. Not every oxygen or nitrogen in every chemical environment is equally available.

A molecule has an O–H group and another molecule has a carbonyl oxygen (C=O). Can they hydrogen-bond?

Usually yes: the O–H hydrogen can donate a hydrogen bond, and the carbonyl oxygen can accept it.

A molecule contains only C–C and C–H bonds. Is it likely to hydrogen-bond strongly with water?

No. It lacks typical hydrogen-bond donors and acceptors and is largely nonpolar, so it is hydrophobic.

A proposed structure gives neutral carbon five ordinary covalent bonds. Is that likely to be a valid biological structure?

Usually no. Neutral carbon typically forms four covalent bonds. Check the valence pattern, formal charges, and whether the model is chemically plausible.

How can you test a molecular drawing for plausible valence?

Count each atom's bonds and lone pairs/charges as appropriate: H usually one bond, O two, N three, C four. Flag impossible counts and check whether formal charges explain exceptions.

What distinguishes prokaryotic from eukaryotic cells?

Prokaryotes lack a membrane-bound nucleus and membrane-bound organelles; their DNA is in a nucleoid region. Eukaryotes have a nucleus and membrane-bound organelles.

Do all prokaryotic cells lack DNA or ribosomes?

No. Prokaryotes have DNA and ribosomes; they simply lack a membrane-bound nucleus and typical membrane-bound organelles.

How do plant and animal cells differ in common introductory models?

Plant cells typically have a cellulose cell wall, chloroplasts in photosynthetic tissues, and a large central vacuole. Animal cells lack cell walls and chloroplasts and often have smaller vesicles/vacuoles.

Define organelle, cytoplasm, and cytosol.

Organelle: specialized cell structure, often membrane-bound. Cytoplasm: contents between the plasma membrane and nucleus, including cytosol and organelles. Cytosol: the fluid portion of the cytoplasm.

What is the nucleus's main function?

Stores most eukaryotic DNA and is a major site of gene regulation and transcription.

What do mitochondria do, and which cells tend to have many?

They perform most cellular aerobic respiration and produce much of the cell's ATP. Cells with high energy demands, such as muscle cells, often have many mitochondria.

What do chloroplasts do, and where are they found?

They carry out photosynthesis in plants and algae. They are common in photosynthetic tissues, such as leaf cells, but not in every plant cell.

What is the rough endoplasmic reticulum (rough ER) specialized for?

It has ribosomes and helps synthesize and process proteins destined for secretion, membranes, or certain organelles.

What is the smooth endoplasmic reticulum (smooth ER) specialized for?

It participates in lipid synthesis, detoxification, and calcium storage, depending on cell type.

What does the Golgi apparatus do?

Modifies, sorts, and packages proteins and lipids into vesicles for delivery to their destinations or secretion.

What do lysosomes do?

Use acidic enzymes to digest and recycle macromolecules, damaged cell parts, and material taken up by the cell.

What are vacuoles used for in plant cells?

The large central vacuole stores water and solutes, helps maintain turgor pressure, and can store or break down materials.

How can organelle abundance help you infer a cell's function?

Look for structures matching the cell's job: many mitochondria suggest high ATP demand; abundant rough ER and Golgi suggest protein production/secretion; many chloroplasts suggest photosynthesis.

A cell model shows abundant rough ER, Golgi, and secretory vesicles. What function is likely prominent?

Producing, processing, and exporting proteins, such as a cell specialized to secrete enzymes or hormones.

A cell model shows many mitochondria but little rough ER. What does this suggest?

High energy demand may be more important than large-scale protein secretion, though organelle abundance alone does not prove a cell's identity.

What is a triglyceride made of, and what is its main role?

One glycerol joined to three fatty acids. Triglycerides are major long-term energy-storage molecules and also provide insulation/cushioning.

What is a fatty acid structurally?

A hydrocarbon chain with a terminal carboxyl group. The chain is mostly nonpolar; the carboxyl group is polar and can be ionized.

How do saturated and unsaturated fatty acids differ?

Saturated fatty acids have no carbon–carbon double bonds in the hydrocarbon chain and are relatively straight. Unsaturated fatty acids have one or more double bonds, often creating kinks.

How does a phospholipid differ from a triglyceride?

A phospholipid typically has glycerol, two fatty-acid tails, and a phosphate-containing polar head. A triglyceride has three fatty-acid tails and is mainly for energy storage.

Why are phospholipids amphipathic?

Their phosphate-containing head is polar/hydrophilic, while their fatty-acid tails are nonpolar/hydrophobic.

What is cholesterol's basic structure and role in animal membranes?

It has a small polar hydroxyl group and a large rigid hydrophobic steroid-ring region plus a hydrocarbon tail. It helps regulate membrane fluidity and stability.

Describe the fluid mosaic model of the plasma membrane.

A dynamic phospholipid bilayer with proteins and other molecules embedded in or associated with it. Lipids and many proteins can move laterally; the membrane is not a rigid, uniform sheet.

How can membrane proteins associate with the lipid bilayer?

Integral proteins are embedded in the bilayer; transmembrane proteins span it. Peripheral proteins associate with the membrane surface or other proteins. Some proteins are lipid-anchored.

Why do phospholipids form a bilayer in water?

Hydrophilic heads interact with water while hydrophobic tails avoid water and pack together. This arrangement lowers the exposure of tails to water.

What happens to amphipathic lipids in a hydrophobic environment?

They may orient their hydrophobic tails toward the surrounding nonpolar environment and shield their polar heads, potentially forming reverse structures such as reverse micelles. The arrangement depends on the molecules and environment.

How does increasing temperature usually affect membrane fluidity?

It increases phospholipid movement and usually increases membrane fluidity.

How do longer fatty-acid tails affect membrane fluidity?

Longer tails generally increase van der Waals contact between tails, making the membrane less fluid at a given temperature.

How do unsaturated tails affect membrane fluidity?

Cis double bonds create kinks that prevent tight packing, generally increasing fluidity.

How does cholesterol affect membrane fluidity?

It buffers fluidity: at high temperatures it restrains phospholipid movement and reduces fluidity; at low temperatures it prevents tight packing and helps prevent solidification.

A membrane model changes from short, unsaturated tails to long, saturated tails. Predict the fluidity change.

Fluidity decreases because longer tails have more intermolecular contact and saturated tails pack more tightly.

Why are biological models useful but potentially misleading?

Models simplify complex systems so patterns are easier to see, but may omit scale, motion, chemical detail, diversity, or exceptions. Ask what the model includes and what it leaves out.

Why is the phospholipid bilayer semipermeable?

Its hydrophobic core lets some small nonpolar molecules cross relatively easily but strongly restricts ions and most large or polar molecules unless a transport pathway is available.

Which molecules cross a pure lipid bilayer most easily, and which cross poorly?

Small nonpolar molecules such as O2 and CO2 cross readily. Ions and large polar molecules cross poorly. Water can cross slowly, but aquaporins can greatly increase its movement.

Define diffusion.

Net movement of particles down their concentration gradient due to random motion, from higher concentration toward lower concentration, until equilibrium is approached.

What is a concentration gradient?

A difference in concentration across space or a membrane. It can drive net movement when the molecule can cross the barrier.

What is simple diffusion?

Passive movement directly through the lipid bilayer, down a concentration gradient, without a transport protein or direct energy input.

What is facilitated diffusion?

Passive movement down a concentration or electrochemical gradient through a membrane protein, such as a channel or carrier. It does not directly require ATP.

How do channels and carriers differ?

Channels create a selective passageway through the membrane. Carriers bind a solute and change shape to move it. Both can mediate facilitated diffusion; carriers often show saturation.

What is active transport?

Transport that moves a substance against its concentration or electrochemical gradient and therefore requires an energy source, directly or indirectly.

What is primary active transport? Give an example.

A transporter uses energy directly, often from ATP hydrolysis, to move a substance against its gradient. Example: the sodium-potassium pump.

What is secondary active transport?

A transporter uses the energy stored in one substance's electrochemical gradient to move another substance against its gradient. The gradient was established by another energy-driven process.

How do symport and antiport differ?

Symport moves two substances in the same direction across a membrane; antiport moves them in opposite directions.

What is osmosis?

Net movement of water across a selectively permeable membrane toward the side with higher effective solute concentration (lower water potential), assuming the solute cannot freely cross.

Define isotonic, hypertonic, and hypotonic relative to a cell.

Isotonic: same effective solute concentration, so no net water movement. Hypertonic: higher effective solute concentration than the cell, so water tends to leave it. Hypotonic: lower effective solute concentration than the cell, so water tends to enter it.

A cell is placed in a hypertonic solution. Predict water movement and cell-volume change.

Water moves out of the cell; the cell shrinks. An animal cell may crenate; a plant cell may lose turgor and plasmolyze.

A cell is placed in a hypotonic solution. Predict water movement and cell-volume change.

Water moves into the cell; an animal cell may swell and potentially lyse. A plant cell becomes turgid because its cell wall resists expansion.

A cell is placed in an isotonic solution. Does water stop moving?

No. Water continues moving both directions, but the rates are equal, so there is no net water movement and average cell volume remains stable.

How do you determine tonicity from a diagram with solute particles on each side of a membrane?

First identify which solutes can cross. Compare the concentrations of nonpenetrating (effective) solutes on each side. Water tends to move toward the side with more effective solute.

A membrane is permeable to water but not to solute X. Side A has 2 units of X and side B has 6 units in equal volumes. Which way is net water movement?

From side A toward side B, because side B has the higher concentration of nonpenetrating solute.

Why is tonicity not always identical to total solute concentration?

Tonicity depends on solutes that cannot freely cross the membrane and therefore sustain an osmotic effect. Permeant solutes may not maintain a lasting difference.

What factors influence the rate and direction of passive transport?

Direction is set by the relevant concentration/electrochemical gradient. Rate depends on gradient size, membrane permeability, surface area, temperature, molecule properties, and availability/number of transport proteins.

Why can a charged ion not simply diffuse through the hydrophobic membrane core?

Moving a charge into the nonpolar core is energetically unfavorable. Ions generally need channels or transporters.

A solute is polar and relatively large, but its concentration is higher outside the cell. Will it necessarily enter by diffusion?

No. A favorable gradient does not overcome the bilayer's permeability barrier by itself. It may need a specific channel or carrier.

A molecule's concentration is equal on both sides of a membrane. What is the net diffusion rate?

Net diffusion is zero at equilibrium, although molecules continue moving randomly in both directions.

A carrier-mediated transport graph plateaus as solute concentration rises. What does the plateau suggest?

Transport is saturating because a limited number of carriers are occupied or cycling at their maximum rate.

How can a cell move glucose into itself against glucose's gradient without directly using ATP at the glucose transporter?

Secondary active transport can couple glucose uptake to movement of an ion down its electrochemical gradient, such as sodium moving down its gradient.

Define metabolism, anabolism, and catabolism.

Metabolism is the sum of chemical reactions in a cell or organism. Anabolism builds complex molecules and generally requires energy. Catabolism breaks molecules down and often releases usable energy.

What is kinetic energy versus potential energy?

Kinetic energy is energy of motion. Potential energy is stored energy due to position, arrangement, or chemical structure.

State the first law of thermodynamics and apply it to a cell.

Energy is conserved: it is transferred or transformed, not created or destroyed. Cells transform energy from food or light into chemical energy and other forms.

State the second law of thermodynamics.

Every energy transfer increases the total entropy of the universe; usable energy becomes more dispersed. A cell can maintain internal order only by taking in energy and releasing heat/waste.

Define free-energy change (ΔG).

ΔG indicates whether a process is thermodynamically favorable under the specified conditions. ΔG < 0 is exergonic; ΔG > 0 is endergonic; ΔG = 0 is equilibrium.

What are enthalpy (H) and entropy (S)?

Enthalpy relates to heat content at constant pressure; entropy describes how energy/matter is dispersed and the number of accessible microscopic arrangements. Their changes help determine ΔG.

How are ΔG, ΔH, ΔS, and temperature related?

ΔG = ΔH − TΔS, where T is absolute temperature in kelvin. Use consistent energy units. The signs of ΔH and ΔS and the temperature determine the sign of ΔG.

A reaction has ΔH < 0 and ΔS > 0. Is it exergonic or endergonic?

ΔG = ΔH − TΔS is negative at all positive temperatures under the simplified assumptions, so it is exergonic.

A reaction has ΔH > 0 and ΔS < 0. Is it exergonic or endergonic?

Both terms make ΔG positive, so it is endergonic at all positive temperatures under the simplified assumptions.

A reaction has ΔH < 0 and ΔS < 0. How does temperature affect favorability?

It is favored at lower temperatures when the negative ΔH dominates; at high temperatures, subtracting TΔS adds a positive term and may make ΔG positive.

A reaction has ΔH > 0 and ΔS > 0. How does temperature affect favorability?

It may be unfavorable at low temperatures but favorable at high temperatures because the −TΔS term becomes more negative as temperature rises.