AP-Biology-Study-Guide

Key Exam Details

• The AP Biology exam is a 3-hour, end-of-course test.
• It includes 60 multiple-choice questions (50% of score) and 6 free-response questions (50% of score).
• Time allotted: 1 hour 30 minutes for each section.
• Course content categories covered:
  • Chemistry of Life: 8–11%
  • Cell Structure and Function: 10–13%
  • Cellular Energetics: 12–16%
  • Cell Communication and Cell Cycle: 10–15%
  • Heredity: 8–11%
  • Gene Expression and Regulation: 12–16%
  • Natural Selection: 13–20%
  • Ecology: 10–15%

Chemistry of Life

• Covers 8–11% of the AP Biology exam.

Water and the Elements of Life

• Water (H2O) consists of two hydrogen molecules covalently bonded to an oxygen molecule.
• Oxygen atom has a slightly negative charge, hydrogen atoms have a slightly positive charge, making water a polar compound.
• Polar nature and shape of water molecules allow hydrogen bonds to form between water molecules.
• Hydrogen bonds are weak bonds between a proton in one molecule and an electronegative atom of another molecule.
• Polar nature of water is crucial for life:
  • Water is a solvent for many other molecules, facilitating distribution of chemicals throughout an organism.
  • Cohesion: molecules of the same kind stick together (hydrogen bond cohesion between water molecules).
    • Causes surface tension: liquid surfaces shrink to minimize surface area.
    • Water droplets form, solid matter floats on water surface.
  • Adhesion: dissimilar molecules are attracted to each other.
    • Responsible for capillary action: liquid moves through spaces, sometimes against gravity.
    • Water is drawn towards the surface it touches due to adhesive forces.
    • Water pulls more water molecules behind it due to cohesive forces.
  • Essential to life on Earth (e.g., capillary action in plants).

Carbon and Organic Molecules

• Carbon, hydrogen, nitrogen, and oxygen make up 99% of living matter.
• Organic molecules (mostly carbon-containing) are the basis of life on Earth.
• Carbon's unique ability to form four bonds with other elements makes it ideal for biological molecules.
• Carbon can form single, double, or triple bonds, resulting in rings, branches, or long chains.
• Carbon is the basis for major biological macromolecules:
  • Carbohydrates
  • Proteins
  • Lipids
  • Nucleic acids
• Nitrogen and phosphorus are also important for nucleic acids and proteins.

The Makeup and Properties of Macromolecules

• Large biological molecules are building blocks of life.
• Key macromolecules: carbohydrates, lipids, proteins, and nucleic acids.
• Carbohydrates, proteins, and nucleic acids are typically polymers: repeating smaller units (monomers).
  • DNA monomers: nucleotides
  • Protein monomers: amino acids
  • Carbohydrate monomers: sugars
• Large polymers are called macromolecules.
• Lipids are generally not polymers, so not always considered macromolecules.
• Macromolecule composition and monomer order affect function.
• Macromolecules form through dehydration synthesis: covalent bond forms between two monomers, releasing water.
• Hydrolysis breaks down polymers into monomers; bond is lysed by water.
• Synthesis reactions use energy stored in covalent bonds of the macromolecule.
• Hydrolysis releases energy for the cell to use.

Proteins

• Proteins comprise the majority of organic molecules in organisms with diverse structures and functions.
• Proteins are made of strings of amino acids connected by covalent bonds.
• There are 20 types of amino acids in biological organisms.

Protein Structure

• Amino acid structure: central carbon atom with:
  • Amino group (NH2)
  • Carboxyl group (COOH)
  • Hydrogen atom
  • R group (determines identity).
• Amino acids are linked by peptide bonds: covalent bonds formed by dehydration synthesis between the carboxy terminus of one amino acid and the amino terminus of the next.
• Polypeptide chain directionality: Amine group at the beginning, carboxyl group at the end.
• Amino acid composition and location confer properties to the resulting protein, affecting its shape.
• Amino acids can be charged, uncharged, hydrophobic, or cause changes in 3D structure.
• Primary structure: amino acid composition and order.
• Secondary structure: protein folding due to interactions between amino acid backbone elements.
  • α helixes: helical structures formed by hydrogen bonds between carbonyl groups of one amino acid and the amino group of another four amino acids down the line.
    • R groups push to the outside of the helix, giving them more opportunity to interact.
  • β sheets: sections of polypeptide chain parallel to each other.
    • R groups presented outward on top and bottom to interact.
• Tertiary structure: interactions between R groups of the same protein.
  • Non-covalent bonds or strong di-sulfide bonds.
  • Minimize free energy of protein by taking the most energetically stable position.
• Quaternary structure: forms between amino acids on different polypeptide chains.
• Protein structures can be denatured (lose higher-order structures) due to changes in pH or temperature.
• Proteins generally return to their proper structures when conditions return to normal (information to form structure retained within polypeptide sequence).

Carbohydrates

• Carbohydrates provide an immediate source of energy and form important structural elements.
• Carbohydrate formula: $(CH2O)n$ , where $n$ is the number of repeating structures.
• Monosaccharides contain 3–7 monomers of $(CH2O)$, connected as a chain or ring (e.g., glucose, fructose, galactose).
• Disaccharides form when two monosaccharides undergo dehydration synthesis and form a covalent bond.
• Covalent bond formed between a carbohydrate and another molecule is called a glycosidic bond.
• Common disaccharides: sucrose, lactose, maltose.
• Polysaccharides are long chains of monosaccharides (linear or branched) and can be made of the same or different monomers.
• Common polysaccharides: starch, chitin, cellulose, and glycogen.

Lipids

• Lipids are nonpolar macromolecules made of hydrophobic hydrocarbon chains (fats, waxes, phospholipids, steroids).
• Lipids are a structural unit of membranes and an energy storage form.
• Fats (triglycerides) are made of a glycerol backbone and three fatty acid chains (hydrocarbons bonded to a carboxyl group).
• Fatty acid chains of triglycerides can vary in length and saturation.
• Saturated fatty acids: all neighboring bonds in the hydrocarbon chain are single bonds, forming straight chains that pack tightly and are solid at room temperature.
• Unsaturated fatty acids: double bonds in the chain.
  • cis fatty acids: hydrogen atoms on the same side of the acid chain, causing a bend (liquid oils at room temperature).
  • trans fatty acids: hydrogen atoms on opposite sides of the fatty acid chain (behave like saturated fats at room temperature but are difficult to metabolize).

The Structure of DNA and RNA

• DNA (deoxyribonucleic acid) is a polymer of nucleotides carrying genetic information.
• Nucleotides are made of a sugar (deoxyribose), a phosphate group, and a nitrogenous base.
• Deoxyribose is a ring structure of oxygen and four carbons, numbered from 1’ to 4’.
• A 5th carbon atom (5’) is bonded to the 4’ carbon of deoxyribose and bonds with the phosphate group.
• Nucleotides are linked together by covalent bonds between the sugar and phosphate groups to make a single strand of DNA.
• Connection between two nucleotides occurs between the 3’ carbon atom of the first nucleotide and the phosphate group of the second; DNA orientation is 3’ to 5’.

DNA Structure

• DNA nucleotides come in four varieties, each with a different base: adenine (A), thymine (T), guanine (G), or cytosine (C).
• In RNA, uracil (U) is used instead of thymine.
• G and A molecules are purines with double nitrogenous rings.
• C, T, and U are pyrimidines with single nitrogenous rings.
• Two strands of DNA with complementary base pairs are linked with hydrogen bonds to form a double helix.
• Base pairing: C-G and A-T (or A-U in RNA) where purines bond with their complimentary pyrimidine.
• Cytosine-guanine connections pair via three hydrogen bonds, adenine-thymine pairs with double hydrogen bonds.
• DNA backbone: sugar and phosphate groups linked together, with nucleotides in the center.
• The bond between the phosphate group and two sugars is a phosphodiester bond.
• Two strands of DNA connect together through complementary base pairing to form a double stranded DNA polymer.
• Two strands of DNA are anti-parallel: one strand will have a 3’-5’ directionality, and the second strand will be oriented in the 5’-3’ direction.

RNA

• RNA (ribonucleic acid) is similar to DNA but has ribose as the sugar group and has uracil (U) instead of thymine.
• RNA is usually single-stranded rather than double-stranded.

Sample Chemistry of Life Questions

*The strongest complementary base pair found in DNA is between
A. adenine and guanine.
B. cytosine and thymine.
C. adenine and thymine.
D. cytosine and guanine.
Explanation:The correct answer is D. Three hydrogen bonds form between cytosine and guanine, making this a stronger complementary base pair than the adenine/thymine base pair. Adenine and guanine are both purines and do not pair up in the DNA double helix; and cytosine and thymine are both pyrimidines and do not pair up in the DNA doub le helix. Finally, while adenine and thymine do pair up in the DNA double helix, there are only two hydrogen bondsthat form between the two. Three hydrogen bonds form between cytosine and guanine, making the latter base pair stronger.

*Water travels up a stem through a process called
A. cohesion-adhesion.
B. cohesion-tension.
C. adhesion-tension.
D. hydrogen bonding.
Explanation:The correct answer is B. As water evaporates from a leaf, a column of water molecules is pulled upward through cohesion-tension. The water molecules are bound together through hydrogen bonding, and the evaporation at the leaf pulls the chain of molecules upward due to the inherent surface tension of water.

*A carboxylic acid contains which of the following functional groups?
A. –OH
B. –CHO
C. –COOH
D. –O–Explanation:The correct answer is C. A carboxylic acid contains the –COOH (carboxyl) functional group. An alcohol contains the –OH (hydroxyl) functional group; an aldehyde containsthe –CHO (aldehyde) functional group; and an ether contains the –O– (ether) functional group.

Cell Structure and Function

• Consists of around 10–13% of questions on the exam.

Cellular Components and Functions

• Cells are the smallest functional unit of life.
• Two categories: prokaryotes and eukaryotes.
  • Prokaryotes: unicellular, no cell walls or membrane-bound organelles, single circular chromosome (bacteria and archaea).
  • Eukaryotes: multiple chromosomes in a membrane-bound nucleus and other organelles (protozoans, yeast, plants, and animals).
• Animal and plant cells differ in several features.
  • Animal cells: thin plasma membrane (phospholipid bilayer with embedded proteins) regulates molecule entry and exit, and facilitates communication.
  • Plant cells: cell wall (cellulose and lignin) provides strength, rigidity, and protection, and helps store water.
    • Cell walls are also in fungi, algae, bacteria, and archaea, but with different compositions.
    • Plants also have a central vacuole, a fluid filled membrane-bound structure that stores water and nutrients for the cell.
    • Plant and animal cells differ in how they produce energy; plant cells contain chloroplasts and mitochondria, while animal cells only have mitochondria.

Eukaryotic Cell Organelles

• Nucleus: contains most of the cell's genetic material (chromatin); site of RNA transcription and processing; contains the nucleolus (where ribosomes are made); encased in a plasma membrane with nuclear pores that restrict movement.
• Mitochondria: membrane-bound organelles where cellular respiration (ATP synthesis from ADP) occurs; double membrane (smooth outer, rough inner); contain their own circular DNA, reproduce within cells, and have their own protein synthesis machinery.
• Chloroplast: membrane-bound organelles containing chlorophyll for photosynthesis; have their own DNA and protein synthesis machinery (like mitochondria).
• Endoplasmic Reticulum (ER): folded, membrane-bound organelles for transport from the nucleus to the Golgi apparatus; rough ER (covered with ribosomes) makes membrane-bound proteins and proteins packaged in vesicles
• smooth ER (no ribosomes) synthesizes lipids, fats, and steroids.
• Golgi Apparatus: stacks of membrane sacks for protein modification, packaging, and export.
• Ribosomes: perform RNA translation into protein; made of ribosomal RNA (rRNA) and proteins; can be free in the cell (making proteins in the cytoplasm) or on the rough ER (synthesizing proteins that end up on or in cell membranes); ribosomes found in every form of life on Earth, providing evidence for a common ancestor.
• Lysosomes & Peroxisomes: vesicles where cell waste is destroyed and recycled; lysosomes contain hydrolytic enzymes that destroy proteins, cell waste, and damaged organelles; peroxisomes destroy lipids and reactive oxygen species.
• Cytoskeleton: microtubules, intermediate filaments, and microfilaments that provide structure, keep organelles in place, help cells move, and provide a framework for protein movement in a cell
• Centrosome: main microtubule organizing center of the cell, organizes mitotic spindle during cell division; a cell has a single centrosome unless it is in the cell cycle.
• Vesicles: membrane sacs that transport molecules in the cell; can carry substances for release, membrane-bound proteins for the cell membrane, and remove pieces of membrane for destruction.

Cell Size

• Cells exchange molecules to sustain life, and must maintain a membrane surface area that supports metabolic needs.
• Cell growth is limited by the surface area of the cell.
• Volume increases faster than surface area.
• Equations for volume and surface area:
  • Sphere:
    • Volume: $V = binom{4}{3}πr^3$
    • Surface Area: $SA = 4πr^2$
  • Cube:
    • Volume: $V = s^3$
    • Surface Area: $SA = 6s^2$
  • Rectangular Solid:
    • Volume: $V = lwh$
    • Surface Area: $SA = 2lh + 2lw + 2wh$
  • Cylinder:
    • Volume: $V = πr^2h$
    • Surface Area: $SA = 2πrh + 2πr^2$
• Metabolically active cells remain small or have specializations for more surface area (e.g., membrane folds).

The Cell Membrane Structure and Function

• The fluid mosaic model describes cell membrane structure.
• Plasma membrane: phospholipid bilayer with cholesterol, proteins, glycolipids, and glycoproteins.
• Components of the membrane are in constant motion.
  • Phospholipids: hydrophilic head (glycerol molecule with a phosphate group) and hydrophobic tails (non-polar fatty acids).
    • Form a bilayer with hydrophilic heads facing aqueous internal and external environments, and hydrophobic ends in the middle.
  • Membrane proteins: traverse the entire membrane (transmembrane proteins), partially extend on one side, or attach loosely.
    • Integral membrane proteins: hydrophobic portion anchors them within the membrane.
    • Peripheral membrane proteins: loosely attached to the membrane via other integral proteins or phospholipids.
  • Glycolipids and glycoproteins: attach to the outer surface of the cell and act as signals for the cell type (e.g., immune system identifiers).
  • Cholesterol groups: embedded within the hydrophobic bilayer and buffer membrane fluidity at low and high temperatures.

Cell Regulatory Mechanisms

• Phospholipid bilayer creates a semipermeable barrier due to hydrophobic interface.
• Selective permeability: only certain molecules can pass through the membrane.
  • Small nonpolar molecules (N2, O2, CO2) pass easily.
  • Uncharged polar molecules (water) pass through in small amounts.
  • Hydrophilic substances (large polar molecules and ions) require membrane transporters.
• Plants and bacteria have cell walls made of complex carbohydrates.

Cell Regulatory Mechanisms

• Cell has several methods to allow transport across the membrane.

  • Passive transport: movement across a membrane without energy use, due to molecule diffusion from high to low concentration.
  • Active transport: movement across a membrane requiring energy to move molecules from low to high concentration.
  • Endocytosis: vesicle forms in a plasma membrane, taking molecules from the external environment into the cell.
  • Exocytosis: vesicle fuses with the membrane and dumps contents into the extracellular space.

• Three forms of passive transport: simple diffusion, facilitated diffusion, and osmosis.

  • Simple diffusion: molecules pass across the membrane freely along the concentration gradient (e.g., oxygen and carbon dioxide).
  • Facilitated diffusion: channels or carrier molecules assist molecules across the membrane (e.g., aquaporins).
  • Osmosis: water moves across a semipermeable membrane from low to high solute concentration to equalize concentrations.

• Osmolarity is the total concentration of solutes in a solution.

• Osmotic pressure is the pressure that pulls water from one side of a membrane to the other.

• Tonicity is the ability of water to move across a membrane by osmosis.

• Cell environments can be isotonic (same solute concentration), hypertonic (more solute outside), or hypotonic (less solute outside).

Active Transport

*Active transport: Cells in a hypotonic solution take on too much water, causing them to swell and potentially burst - cells in a hypertonic solution are at risk of shriveling.

• Active transport mechanisms use metabolic energy (often ATP) to transport molecules.
• Active transport maintains concentration gradients across cells.
• Neurons use concentration gradients to signal to each other, such as internal environment being high potassium+ and low sodium+ and external environment is low potassium+ and high sodium+.
• These concentration differences create a negative membrane potential that positions it to respond to stimulation.
• The cell then uses active mechanisms - Na+/K+ ATPase, using ATP to move sodium and potassium+ across the membrane in an energetically unfavorable direction to maintain the concentration difference and membrane charge.

Cellular Compartmentalization

• Compartmentalization of processes is an essential feature of cellular environments, and membranes allow cells to compartmentalize processes that need to be kept separated from the rest of the environment.
• The lytic enzymes in lysosomes would be fatal to the cell if released into the cytosol.
• The membranes create internal environments that are different than the external environment.
• For neurons to fire action potentials, they take advantage of an electrochemical gradient where the internal environment is rich in potassium and the external environment is rich in sodium.
• Without membranes that actively maintain these different environments, neurons would not function.
• Internal membranes also facilitate processes by increasing reaction surface areas and keeping molecules in the places that they are needed to function.
• Mitochondria are formed to maximize internal membrane surface area, so they can form more ATP.
• Membrane bound organelles evolved from prokaryotic cells through a process called endosymbiosis, and the theory is that organelles like chloroplasts and mitochondria were once free-living prokaryotes:
  • A eukaryotic cell engulfed a prokaryote—likely a photosynthetic autotroph—but did not digest it.
  • This generated a mutually beneficial relationship where the prokaryote generated energy for the eukaryotic cell, and the eukaryotic cell protected the prokaryotic cell and provided nutrientsfor it.
  • Over time, this relationship became permanent as the prokaryotic cell stopped carrying all of the genes needed for its survival and the eukaryotic cell became dependent on the energy the prokaryotic cell provided.
  • Supported through the fact that both share features of prokaryotic cells, like having their own circular DNA genome.
• Prokaryotes generally do not have membrane bound organelles—rather, they have regions with specialized structures and functions within them.

Sample Cell Structure and Function Questions

• A cell that produces and secretes a large number of proteins would probably have
  A. extensive rough ER.
  B. limited rough ER.
  C. few mitochondria.
  D. a cell wall.
  Explanation: The correct answer is A. The rough ER (endoplasmic reticulum) is responsible for producing proteins (in the bound ribosomes) and transporting them within and outside the cell.

• When a solution has a lower solute concentration than the solution on the other side of a membrane, that solution is said to be
  A. hypotonic.
  B. isotonic.
  C. hypertonic.
  D. undergoing osmosis.
  Explanation: The correct answer is A. A hypotonic solution has a lower solute concentration than the solution on the other side of a membrane. A hypertonic solution has a higher solute concentration than the solution on the other side of a membrane.. Choice D is incorrect because osmosis is the term for the diffusion of water across a membrane.

*What feature of a plant cell prevents it from bursting when in a highly aqueous solution?
A. a large central vacuole
B. a guard cell
C. a cell wall
D. chloroplasts
Explanation: The correct answer is C. The rigid cell wall of plant cells prevents lysis of the cell when in an aqueous environment. The vacuole of the cell expands, creating turgor pressure, but the cell membrane expands only as much as the cell wall will allow. Choice B is incorrect because guard cells surround stomata in leaves and regulate transpiration from the leaf. Choice D is incorrect because chloroplasts are the site of photosynthesis in the cell and are located within the cytoplasm.

Cellular Energetics

Consists of around 12–16% of questions on the AP Exam

The Structure and Function of Enzymes

• Energy releasing reactions have an energy barrier to be overcome first, the activation energy, otherwise cells would release energy indefinitely.
• Catalysts reduce activation energy and increase reaction rate without itself undergoing a chemical change. Biological catalysts are Enzymes.
• Enzymes act by changing the conformation of molecules that they interact with to put them into a more optimal state for a reaction to proceed.
• The active site of an enzyme is the portion that interacts with the molecule, and the substrate is the molecule that the enzyme binds with to facilitate a change.
• Enzymes and molecules in a biological reaction are affected by their environment such as increases in heat generally cause reactions to take place faster because increased molecule movement increases the frequency of collisions between substrate and enzyme, however, excessive heat can denature proteins, by altering hydrogen bonds and thus inhibiting their ability to take part in a reaction. . Similarly, pH can alter the efficiency of a reaction by altering hydrogen bonds effects, which can be reversible if the conditions return to baseline. The concentration of substrates in comparison to enzymes will also affect enzyme activity.
• Inhibitors, such as, competitive inhibitors that compete for the active site of an enzyme by, keeping it from binding the substrate and blocking the reaction or Noncompetitive inhibitors that bind to other sites on the enzyme, changing the enzyme’s conformation and keeping it from efficiently binding the substrate.

The Role of Energy in Living Systems

• Bioenergetics is the study of energy transformation in living organisms
• Metabolism is the general term for all energy transformations in living organisms, including processes like photosynthesis, mitochondrial respiration, and movement.
• In biological systems, energy input constantly exceeds loss to keep the systems going and stored in the form of molecules that contain chemical bonds that can be broken down, most often in the form of sugars or fats.
• Anabolism is the process where molecules store energy in the form of chemical bonds, and catabolism is the process by which energy is released by breaking these bonds.
• To prevent wasting precious energy for mall tasks, larger energy forms are generally first converted to smaller energy molecules - Adenosine triphosphate (ATP) is the primary source of energy that cells use to function.
• ATP can be broken down into ADP (adenosine diphosphate) and AMP (adenosine monophosphate), through process like fermentation and respiration, where energy is released at both steps that can be harnessed to power other cellular processes by being linked to most cellular processes, providing a streamlined way for cells to harness energy.

The Processes of Photosynthesis

• Photosynthesis is the process where light energy is converted to cellular energy in the form of glucose.
• During photosynthesis, carbon dioxide, water, and light are converted to glucose and oxygen:
  $6CO2 + 6H2O + Light → C6H12O6 + 6O2$
• Photosynthesis initially evolved in cyanobacteria, resulting in oxygenation of the Earth’s atmosphere.
• Photosynthesis takes place in two main phases:
  • Photolysis (the light dependent reaction)
  • Calvin cycle (the light independent reaction).

Photolysis and The Calvin Cycle

• Photolysis takes place in the thylakoid membranes of chloroplasts. During this step, light energy is absorbed by chlorophylls, which then generate ATP and NADPH (an electron carrier used in biological reactions.) Water is used in this reaction and oxygen is released.
• The Calvin cycle takes place in the stroma of chloroplasts, where carbon dioxide from the environment reacts with ATP and NADPH generated in photolysis to create small 3 carbon sugars, which are then joined to form glucose.
• Glucose provides the cell with both energy, as it can be used to synthesize ATP, and fixed carbon, organic carbon molecules, like sugars, used by cells to build molecules needed in cells for other processes.
• The Calvin cycle both removes carbon from the atmosphere and fixes the energy generated from photolysis in a form that can be stored in cells for later use.

Photosystems in the Light Dependent Reaction

• The light dependent reaction relies on photosystems to harvest light energy. Light is absorbed by two photosystems that harness the electrons from water to make NADPH and ATP from NADP+ and ADP during Non-cyclic phosphorylation.
• There are two photosystems, photosystem I (PSI) and photosystem II (PSII) composed of a light harvesting complex of proteins and hundreds of chlorophylls and pigments, and a special pair of chlorophyll a at the core.
• During non-cyclic phosphorylation, light energy is first harnessed by PSII through the light harvesting complex, and passed via PSII’s special pair of chlorophyll a (called P680) boosting an electron to a higher energy level, then passed to an acceptor molecule and replaced with an electron taken from water, releasing oxygen.
• The high energy electron is passed along the membrane by a series of transporters, called the electron transport chain (ETC) loosing a little energy at each step, some of this energy is used to pump H+ ions from the stroma into the thylakoid membrane where the pumping creates a proton gradient that is linked to formation of ATP from ADP through a process called chemiosmosis via an enzyme called ATP synthase, phosphorylation of ADP to generate ATP in photosynthesis is called photophosphorylation.
• PSI receives the excited electron, which is passed along the ETC, and light energy received by PSI is used to excite the electron through its special chlorophyll pair (called P700) The electron, now at a very high energy level, is then passed by an acceptor molecule which passes it along another electron transport chain that results in the creation of NADPH from NADP+ ATP and NADPH generated in during the light cycle are then used in the stroma of chloroplasts to generate sugar from carbon dioxide through the Calvin cycle.

The Processes of Cellular Respiration

All forms of life use respiration and fermentation to break down biological macromolecules, like sugars and fats, into ATP. In eukaryotes, cellular respiration breaks down glucose into carbon dioxide and water to generate ATP. As in photosynthesis, cellular respiration takes place in a series of steps where energy is passed along an electron transport chain.

• Step 1: In the first step of respiration, called glycolysis, the 6-carbon containing glucose is broken down into two 3-carbon pyruvates, two ATP molecules, and two NADH molecules.
  *During glycolysis, an ADP is converted to ATP and NAD+ is converted to NADH. Glycolysis takes place in the cell’s cytosol.
• Step 2: After glycolysis, the pyruvate molecules are transported into mitochondria, where they are broken down into two carbon molecules, called acetyl groups, that are bound to coenzyme-A, in a molecule called acetyl CoA.
  *This step, called pyruvate oxidation, reduces NAD+ to NADH, but does not generate ATP.
• Step 3: Acetyl CoA then moves into the citric acid cycle, also called the Krebs cycle. T
  *he citric acid cycle is a form of aerobic respiration where acetyl co-A, which is a product of oxidized pyruvate, is metabolized to produce one NADH, one FADH2, two carbon dioxides, and either one ATP or one GTP
• Step 4: In the final step of cellular respiration, called oxidative phosphorylation, NADH and FADH2 are then used to make more ATPs through an electron transport chain in the membrane of mitochondria.
  *As in photosynthesis, the electron transport chain uses electrons donated by carrier molecules, in this case, NADH and FADH2, which are then passed along the chain. As electrons are passed along, they lose some energy, which is used to pump H+ ions from the mitochondrial matrix to the intermembrane space. This creates a chemical gradient, which is used to convert ADP to ATP through chemiosmosis by ATP synthase. The final electron acceptor in oxidative phosphorylation is an O2 molecule, which generates water. In prokaryotes, the first three steps of respiration take place in the cytosol and oxidative phosphorylation takes place in the cell’s membrane.
  *Some anerobic prokaryotes other proton acceptors are used at the end of the electron transport chain in a process called anaerobic cellular respiration.
  *In some cells, the electron transport chains are decoupled from the generation of ATP often to generate heat to warm the body instead of energy storage.

Fermentation and Molecular Diversity

• If oxygen is not available at the end of the electron transport chain to accept electrons, cells take a slightly different approach to respiration. During fermentation, glycolysis proceeds, but pyruvates are converted to other organic molecules like lactic acid and alcohol.
  *This regenerates NAD+ from NADH, which allows glycolysis to continue.

*Molecular Diversity and Cellular Response to Environmental Changes exists in the for of several mechanisms for life to generate ATP, such as plants having a variety of types of chlorophyll in their cells that can harness energy from different wavelengths of light.

Sample Questions Cellular Energetics

• Enzymes lower the _ of a reaction.
  A. temperature
  B. activation energy
  C. free energy
  D. speed

  Explanation: The correct answer is B. Enzymes lower the activation energy of a reaction, or the energy needed for a reaction to proceed.

• The light-dependent reactions of photosynthesis transform energy from sunlight into chemical energy in the form of
  A. photons.
  B. pyruvic acid.
  C. lactic acid.
  D. electrons.
  *Explanation: The correct answer is D. Electrons generated in photosynthesis are used to produce energy in
  the form of ATP or NADPH.

• Which of the following is a product of anaerobic respiration?
  A. pyruvic acid
  B. lactic acid
  C. glucose
  D. oxygen
  *Explanation: The correct answer is B. In anaerobic respiration, pyruvic acid molecules are broken down into end products.

Cell Communication and Cell Cycle

• Around 10–15% of the questions on your AP exam will cover the topic Cell Communication and Cell Cycle.

The Mechanisms of Cell Communication

• Cells communicate to each other through both long-range and short-range signals. These types of messages often occur through one cell releasing a molecule in the extracellular space, called a ligand, that is then received by another cell that has a receptor for that ligand. There are four methods of cell communication:
  • Paracrine signaling occurs when one cell releases ligand into the extracellular space to signal to nearby cells. This type of signaling occurs at neuronal synapses when an axon terminal releases neurotransmitter on a receiving neuron.
  • Autocrine signaling occurs when a cell releases a signal to itself. This is one way that cells regulate their own growth and intracellular processes.
  • Endocrine signaling occurs when a cell releases a ligand, typically into the bloodstream, to affect cells a long way away. This is normally how hormones work.
  • Signaling through cell-cell contact occurs when two cells physically contact each other, and this causes a signal to be passed on. This can occur through gap junctions on cells, which are physical connections between two cells that allow them to exchange small signaling molecules, or through binding of ligands and receptors on the surfaces of two adjacent cells. Cell surface binding is an important way that the immune system uses to recognize pathogens and mount a response against them.

Signal Transduction and Cellular Responses and Feedback

• When a cell receives a signal, it must have a way to respond to it. Signal transduction pathways link the signal to the appropriate response. Signal transduction begins when a ligand is recognized by a receptor. Ligands can be simple molecules like small chemicals, small peptides, or large proteins.
• Receptors generally recognize one or a few ligands and have several forms such as, intracellular receptors that reside within the cell , Hormone receptors and cell surface receptors that reside within the plasma membrane and respond to signals from the outside, including ligand-gated ion channels, G-protein coupled receptors, and enzyme-linked receptors:

Intracellular and Cell Surface Receptors

• Intracellular receptors reside within the cell, with Hormone receptors as an important example of these that when hormones bind a receptor, the receptor changes shape and enters the nucleus to induce changes in gene expression.
  *G -protein coupled receptors respond to a signal by activating their coupled G-protein, which, interacts with other proteins within the cell, causing other events to occur/ the olfactory system relies on G-protein coupled receptors to transduce different odorants into smells that we recognize.
• Enzyme-linked receptors are a type of receptor that are coupled to an enzyme. Once activated, the enzyme is able to induce reactions within the cell.
• Once a receptor is activated by a ligand, a signaling cascade is initiated that causes changes within the cell such as inducing gene expression, secreting a molecule, changes in cell growth, or changes in the identity of the cell.

Cellular Responses and Feedback Mechanisms

• Feedback mechanisms are used in biological systems to maintain their internal environments and respond quickly to changes such as through Negative feedback mechanisms that help to return a system to its set point after a disruption and return to homeostasis, while Positive feedback happens when the response to a signal amplifies that response so that there is a quick change moving an organism away from equilibrium.
• The Events in a Cell Cycle: The cell cycle is the process that cells undergo to grow, duplicate their DNA, and make two cells with identical DNA. In eukaryotic cells, the cell cycle includes interphase, mitosis, and cytokinesis.

Phases of Interphase

Steps are as follows:
1.Gap 1 (G1): The cell grows in size, copies organelles, and synthesizes the molecules it will need to divide.
2.S phase: