Unit 1: Chemistry of Life

Elements

• Elements: are substances that cannot be broken down into simpler substances by chemical means.

• Oxygen (O), carbon (C), hydrogen (H), and nitrogen (N).

• These four elements are used to build biological molecules, such as carbohydrates, proteins, lipids, and nucleic acids. They are also used to form storage compounds and cells in all organisms.

• Some elements are known as trace elements because they are required by an organism only in very small quantities. They include iron (Fe), iodine (I), and copper (Cu).

• Other elements are present but in smaller quantities.

Subatomic Particles

• Atoms are the unit of life and are the building blocks of the physical world.

  • Protons are positively charged (+) particles

  • Neutrons are uncharged particles.

  • Electrons are negatively charged (–) particles

• Some atoms have the same number of protons but differ in the number of neutrons in the nucleus. These are called isotopes.

Compounds

• Consists of two or more elements

• The atoms of a compound are held together by chemical bonds, which may be ionic bonds, covalent bonds, or hydrogen bonds.

• An ionic bond is formed between two atoms when one or more electrons are transferred from one atom to the other.

• The charged forms of the atoms are called ions.

• A covalent bond is formed when electrons are shared between atoms. If the electrons are shared equally between the atoms, the bond is called non-polar covalent. If the electrons are shared unequally, the bond is called polar covalent.

Water: The Versatile Molecule

• Hydrogen bonds are weak chemical bonds that form when a hydrogen atom that is covalently bonded to one

• The hydrogen bonds that hold water molecules together contribute to a number of special properties, including cohesion, adhesion, surface tension, high heat capacity, and expansion on freezing.

• Water molecules have a strong tendency to stick together. This exhibits cohesive forces.

• Water molecules also like to stick to other substances—This makes them adhesive

• These two forces taken together—cohesion and adhesion—account for the ability of water to rise up the roots, trunks, and branches of trees. This is capillary action.

• The cohesion of water molecules contributes to another property of water known as surface tension. The surface of the water has tension to it. The water molecules are stuck together, and light things like leaves and water striders can sit atop the surface without sinking.

Acids and bases

• Reactions are also influenced by whether the solution in which they occur is acidic, basic, or neutral.

• A solution is acidic if it contains a lot of hydrogen ions (H+). If you dissolve an acid in water, it will release a lot of hydrogen ions.

• Bases do not release hydrogen ions when added to water. They release a lot of hydroxide ions (OH–).

• The acidity or alkalinity of a solution can be measured using a pH scale. The pH scale is numbered from 1 to 14. The midpoint, 7, is considered neutral pH.

• The concentration of hydrogen ions in a solution will indicate whether it is acidic, basic, or neutral.

  • pH = –log [H+]

• The pH scale is logarithmic and represents a tenfold change in hydrogen ion concentration.

Organic molecules

• Molecules with carbon are organic molecules and molecules that do not contain carbon atoms are called inorganic compounds.

• Carbon is important for life because it is a versatile atom, meaning that it has the ability to bind not only with other carbons but also with a number of other elements including nitrogen, oxygen, and hydrogen

• Polymers are chains of building blocks in macromolecules

• Monomers are the individual building blocks of a polymer

• Polymers are formed through dehydration synthesis (or condensation) reactions. A water molecule is lost in the reaction, and a larger compound is formed.

• Hydrolysis is when polymers can also be broken down into monomers.

• The water breaks the bond between the two monomers.

• Four classes of organic compounds central to life on Earth:

  1. carbohydrates

  2. proteins

  3. lipids

  4. nucleic acids

Carbohydrates

• Carbohydrates are organic compounds that contain carbon, hydrogen, and oxygen. They are in a ratio of approximately 1:2:1

• Most carbohydrates are categorised as either monosaccharides, disaccharides, or polysaccharides. The term saccharides means “sugar.” The prefixes refer to the number of sugars in the molecule.

Monosaccharides:

• It is an energy source for cells.

• The two most common sugars are glucose and fructose. Their chemical formula is C6H12O6

• Glucose is an important part of the food we eat, and it is the product made by plants during photosynthesis.

• Glucose and fructose can be depicted as either “straight” or “rings.” They have OHs and Hs attached to them.

Disaccharides

• When two monosaccharides are joined, the bond is called a glycosidic linkage, and the resulting sugar is called a disaccharide. The disaccharide formed from two glucose molecules is maltose.

• To break up the disaccharide and form two monosaccharides - Just add water.

Polysaccharides

• Polysaccharides are made up of many repeated units of monosaccharides.

• They can consist of branched or unbranched chains of monosaccharides. Need to know for the test : starch, cellulose, and glycogen.

• Glycogen and starch are sugar storage molecules. Glycogen stores sugar in animals and starch stores sugar in plants.

• Cellulose, on the other hand, is made up of β-glucose and is a major part of the cell walls in plants. Its function is to lend structural support.

• Chitin, a polymer of β-glucose molecules, serves as a structural molecule in the walls of fungus and in the exoskeletons of arthropods.

Proteins

• Proteins are important for structure, function, and regulation of your tissues and organs.

• Amino acids are building blocks of proteins. They contain carbon, hydrogen, oxygen, and nitrogen atoms. There are 20 different amino acids.

• Proteins have four important parts around a central carbon:

  • An amino group (–NH2), a carboxyl group (–COOH), a hydrogen, and an R-group.

• Amino acids differ only in the R-group, which is also called the side chain.

• When it comes to spotting an amino acid, look for the amino group (NH2), then look for the carboxyl molecule (COOH).

• Side chain polarity affects whether an amino acid is more hydrophobic or more hydrophilic.

• The AP Exam divides them into 3 broad categories: hydrophobic (non-polar and uncharged), hydrophilic (polar and uncharged), and ionic (polar and charged).

• Of the common amino acids:

  • Two (glutamic acid and aspartic acid) donate a proton, making them negatively charged.

  • Two (lysine and arginine) accept a proton at physiological pH, which makes them positively charged.

• Two contain the atom sulphur: methionine and cysteine.

Polypeptides

• When two amino acids join, they form a dipeptide. The carboxyl group of one amino acid combines with the amino group of another amino acid.

• The bond between two amino acids is peptide bond.

• If a group of amino acids is joined together in a “string,” the resulting organic compound is called a polypeptide. Once a polypeptide chain twists and folds on itself, it forms a 3D structure called a protein.

• The linear sequence of the amino acids is the primary structure of a protein.

• When the polypeptide begins to twist it begins forming either a coil (known as an alpha helix) or zigzagging pattern (known as beta-pleated sheets). These are secondary structures.

• When the secondary structure reshapes the polypeptide, amino acids that were far away in the primary structure arrangement can now also interact with each other. This is called the tertiary structure.

• When different polypeptide chains sometimes interact with each other, they form a quaternary structure. Haemoglobin is a molecule in the blood that helps distribute oxygen to the tissues in the body. It is formed when four separate polypeptide chains interact with each other and is a quaternary structure.

Liplids

• This consists of carbon, hydrogen, and oxygen atoms.

• The most common examples of lipids are triglycerides, phospholipids, and steroids.

• Lipids are important due to their non-polar structures, they function as structural components of cell membranes, sources of insulation, signalling molecules, and a means of energy storage.

• Our bodies store fat in tissue called, adipose, which is made of cells called adipocytes; these cells are filled with lipids called triglycerides.

• Each triglyceride is made of a glycerol molecule (also called the glycerol backbone) with three fatty acid chains attached to it. A fatty acid chain is covered in hydrogen. One end of the chain has a carboxyl group.

• A fatty acid can be saturated with hydrogens along its long carbon chain or it can’t be unsaturated. If there is a double bond in the chain it is an unsaturated fatty acid.

• Lipid Saturation:The extent of saturation in a lipid can affect its structure and function. The more double bonds that exist within a lipid, the more unsaturated it is.

Phospholipids

• Phospholipids contain two fatty acid “tails” and one negatively charged phosphate “head”.

• Phospholipids are important because of some unique properties they possess, regards to water.

• The two fatty acid tails are hydrophobic. The reason for this is that fatty acid tails are non-polar, and non-polar substances don’t mix well with polar ones, such as water.

• The phosphate “head” of the lipid is hydrophilic, meaning that it does mix well with water since it carries a negative charge, and this charge draws it to the positively charged end of a water molecule.

• A phospholipid has both a hydrophilic region and a hydrophobic region which makes it is an amphipathic molecule.

Cholesterol

• Cholesterol is a four-ringed molecule that is found in membranes.

• It generally increases membrane fluidity, except at very high temperatures. Cholesterol is also important for making certain types of hormones and for making vitamin D.

Nucleic Acids

• They contain carbon, hydrogen, oxygen, and nitrogen and phosphorus. Nucleic acids are molecules that are made up of simple units called nucleotides.

• DNA contains the hereditary “blueprints” of all life. RNA is essential for protein synthesis

Unit 2: Cell Structure and Function

Living things

• Cell is life’s basic unit of structure and function

• As cells increase in volume, the surface area-to-volume ratio decreases, and the exchange of materials becomes less efficient. The surface area and volumes of cells can be calculated using typical geometry formulas.

• The surface area-to-volume ratio concept can also be applied to organisms. As organisms increase in size, their ratio will decrease and this can affect properties of the organism, such as heat-exchange with their surroundings. Small organisms lose heat at much higher rates than larger organisms as a result of their efficient exchange of heat.

Types of cells and organelles

• Light microscopes are used to study stained or living cells. They can magnify the size of an organism up to 1,000 times.

• Electron microscopes are used to study detailed structures of a cell that cannot be easily seen or observed by light microscopy.

• There are two distinct types of cells: prokaryotic cells and eukaryotic cells.

Prokaryotic cell

• It is a lot smaller than a eukaryotic cell and simpler. Bacteria and archaea are examples of prokaryotes.

• The inside of the cell is filled with a substance called cytoplasm.

• The genetic material in a prokaryote is one continuous, circular DNA molecule that is found free in the cell in the nucleoid.

• Most prokaryotes have a cell wall composed of peptidoglycans that surrounds a lipid layer called the plasma membrane.

• Prokaryotes also have small ribosomes.

• Some bacteria may also have one or more flagella, which are used for motility and they might have a thick capsule outside their cell wall for extra protection.

• Prokaryotes do not have any membrane-bound organelles. Their only membrane is the plasma membrane

Eukaryotic cell

• Eukaryotic cells are more complex. Fungi, protists, plants, and animals are examples of eukaryotes.

• Eukaryotic cells have many smaller structures called organelles. Some of these organelles are the same structures seen in prokaryotic cells, but many are uniquely eukaryotic.

Plasma Membrane

• It is the outer envelope of the cell, made up of mostly phospholipids and proteins.

• The plasma membrane is important because it regulates the movement of substances into and out of the cell. The membrane is semipermeable.

• Many proteins are associated with the cell membrane. Some of these proteins are loosely associated with the lipid bilayer (peripheral proteins). They are located on the inner or outer surface of the membrane.

• Others are firmly bound to the plasma membrane (integral proteins). These proteins are amphipathic.

• Some integral proteins extend all the way through the membrane (transmembrane proteins).

• This arrangement of phospholipids and proteins is known as the fluid- mosaic model.

• Adhesion proteins form junctions between adjacent cells.

• Receptor proteins such as hormones, serve as docking sites for arrivals at the cell.

• Transport proteins form pumps that use ATP to actively transport solutes across the membrane.

• Channel proteins form channels that selectively allow the passage of certain ions or molecules.

• Cell surface markers such as glycoproteins, and some lipids, such as glycolipids, are exposed on the extracellular surface and play a role in cell recognition and adhesion. .

• Carbohydrate side chains are found only on the outer surface of the plasma membrane

The Nucleus

• The nucleus is usually the largest organelle in the cell. The nucleus not only directs what goes on in the cell, but is also responsible for the cell’s ability to reproduce. It’s the home of the hereditary information—DNA—which is organized into large structures called chromosomes. The most visible structure within the nucleus is the nucleolus, which is where rRNA is made and ribosomes are assembled.

Ribosomes

• The ribosomes are sites of protein synthesis. Their job is to manufacture all the proteins required by the cell or secreted by the cell. Ribosomes are round structures composed of two subunits, the large subunit and the small subunit. The structure is composed of ribosomal RNA (rRNA) and proteins. Ribosomes can be either free floating in the cell or attached to another structure called the endoplasmic reticulum (ER)

Endoplasmic Reticulum (ER)

• The ER is a continuous channel that extends into many regions of the cytoplasm and provides mechanical support and transportation. The rough ER compartmentalises the cell.

• The region of the ER that lacks ribosomes is called the smooth ER. The smooth ER makes lipids, hormones, and steroids and breaks down toxic chemicals.

Golgi Complex

• After the ribosomes on the rough ER have completed synthesizing proteins, the Golgi complex modify, process, and sort the products.

• They’re the packaging and distribution centers for materials destined to be sent out of the cell. They package the final products in little sacs called vesicles, which carry products to the plasma membrane.

Mitochondria

• They’re power stations responsible for converting energy from organic molecules into useful energy for the cell. The most common energy molecule in the cell is adenosine triphosphate (ATP).

• It consists of an inner portion and an outer portion. The inner mitochondrial membrane forms folds known as cristae and separates the innermost area (the matrix) from the inter-membrane space. The outer membrane separates the inter-membrane space from the cytoplasm.

Lysosomes

• They have sacs that carry digestive enzymes, which they use to break down old, worn-out organelles, debris, or large ingested particles.

• Lysosomes are made when vesicles containing specific enzymes from the trans Golgi fuse with vesicles made during endocytosis. Lysosomes are also essential during programmed cell death called apoptosis.

Vacuoles

• They are fluid-filled sacs that store water, food, wastes, salts, or pigments. Vacuoles serve multiple functions in plant cells.

Peroxisomes

• Peroxisomes are organelles that detoxify various substances, producing hydrogen peroxide (H2O2) as a byproduct. They have enzymes that break down hydrogen peroxide into oxygen and water.

Cytoskeleton

• The shape of a cell is determined by a network of protein fibers called the cytoskeleton. The most important fibers are microtubules and microfilaments.

• Microtubules are made up of the protein tubulin, participate in cellular division and movement.

• Microfilaments are important for movement. These thin, rodlike structures are composed of the protein actin. Actin monomers are joined together and broken apart as needed to allow microfilaments to grow and shrink.

Cilia and Flagella

• Cilia and flagella have locomotive properties in single-celled organisms. The beating motion of cilia and flagella structure allows it to move.

Plant Cells Versus Animal Cells

• Plant cells, unlike animal cells, have a cell wall (made of cellulose). A cell wall is a rigid layer just outside the plasma membrane that provides support for the cell.

• Plant cells possess chloroplasts, which have a double outer membrane. Chloroplasts contain chlorophyll, which gives plants their characteristic green color.

• Cytoplasm within a plant cell is usually taken up by a large vacuole which is the central vacuole.

• Plant cells also differ from animal cells in that plant cells do not contain centrioles.

Transport: traffic across membranes

• The ability of molecules to move across the cell membrane depends on:

  1. the semipermeability of the plasma membrane

  2. the size and charge of particles that want to get through

• Small substances cross the membrane without any resistances since “like dissolves like.” The lipid bilayer has hydrophilic outside and hydrophobic on the inside so only hydrophobic things can pass that central zone. If a substance is hydrophilic, the bilayer won’t let it pass without assistance, called facilitated transport

• Aquaporins are water-specific channels. Glucose and ions such as Na+ and K+ are also transported across the plasma membrane via membrane proteins. Membranes may become polarised as these ions move across them.

Passive Transport: Simple and Facilitated Diffusion

• If there is a high concentration of something in one area, it will move to spread out and diffuse into an area with a lower concentration. The substance moves down a concentration gradient. This is called diffusion.

• When the molecule that is diffusing is hydrophobic, the diffusion is called simple diffusion because the small non-polar molecule can just drift right through the membrane without trouble.

• When the diffusion requires the help of a channel-type protein, it is called facilitated diffusion.

• Anytime that a substance is moving by diffusion, it is called passive transport because there is no outside energy required to power the movement.

Osmosis

• The only difference is that in diffusion the membrane is usually permeable to solute, and in osmosis it is not.

• In plants, the cell wall is important to protect it against osmotic changes, while the cell membrane can shrink away from the wall (a process called plasmolysis) if it loses water and can expand and squeeze tightly against the cell wall if it takes in water.

• Tonicity is used to describe osmotic gradients.

• If an environment is isotonic to the cell, the solute concentration is the same inside and outside.

• A hypertonic solution has more total dissolved solutes than the cell, while a hypotonic solution has less.

• Water potential (Ψ) is the measure of potential energy in water and describes the eagerness of water to flow from an area of high water potential to an area of low water potential.

• It is affected by: pressure potential (Ψp) and solute potential (Ψs)

Solute Potential of a Solution Ψs = −iCRT where: i = ionization constant C = molar concentration R = pressure constant T = temperature in Kelvin (°C + 273)

Adding a solute lowers the water potential of a solution, causing water to be less likely to leave this solution and more likely to flow into it. The more solute molecules present, the more negative the solute potential is.

Active Transport

• Movement against the natural flow is called active transport.

• Some proteins in the plasma membrane are powered by ATP.

• An example of active transport is a special protein called the sodium-potassium pump. It ushers out three sodium ions (Na+) and brings in two potassium ions (K+) across the cell membrane. This pump depends on ATP to get ions across that would otherwise remain in regions of higher concentration.

• Primary active transport occurs when ATP is directly utilised to transport something.

• Secondary active transport occurs when something is actively transported using the energy captured from the movement of another substance flowing down its concentration gradient.

Endocytosis

• When the particles that want to enter a cell are just too large, the cell uses a portion of the cell membrane to engulf the substance. The cell membrane forms a pocket, pinches in, and eventually forms either a vacuole or a vesicle. This process is called endocytosis.

• Three types of endocytosis : pinocytosis, phagocytosis, and receptor- mediated endocytosis.

• Pinocytosis: the cell ingests liquids.

• Phagocytosis: the cell takes in solids.

• Receptor-mediated endocytosis: involves cell surface receptors that work in tandem with endocytic pits that are lined with a protein called clathrin. When a particle, or ligand, binds to one of these receptors, the ligand is brought into the cell by the invagination, or “folding in” of the cell membrane. A vesicle then forms around the incoming ligand and carries it into the cell’s interior.

Bulk Flow

• Bulk flow is the one-way movement of fluids brought about by pressure.

• Example: movement of blood through a blood vessel and the movement of fluids in xylem and phloem of plants are examples of bulk flow.

Dialysis

• Dialysis is the diffusion of solutes across a selectively permeable membrane.

• Kidney dialysis is a specialized process by which the blood is filtered by using machines and concentration gradients.

Exocytosis

• In exocytosis, a cell ejects waste products or specific secretion products, such as hormones, by the fusion of a vesicle with the plasma membrane, which then expels the contents into the extracellular space. Exocytosis is basically reverse endocytosis.

Unit 3: Cellular Energetics

Bioenergetics

The study of how cells accomplish this is called bioenergetics.

Thermodynamics

Energy cannot be created or destroyed, it can be only be transferred.

• First Law of Thermodynamics: Cells cannot take energy out of thin air. It must harvest it from somewhere.

• Second Law of Thermodynamics: It states that energy transfer leads to less organization. That means the universe tends toward disorder (entropy). In order to power cellular processes, energy input must exceed energy loss to maintain order. Cellular processes that release energy can be coupled with cellular processes that require an input of energy.

Types of Reactions

• Exergonic reactions are those in which the products have less energy than the reactants.

• The course of a reaction can be represented by an energy diagram. You’ll notice that energy is represented along the y-axis.

• Reactions that require an input of energy are called endergonic reactions. You’ll notice that the products have more energy than the reactants.

Enzymes

• A catalyst is something that speeds something up.

• Enzymes are biological catalysts that speed up reactions which is by lowering the activation energy and helping the transition state to form.

• Enzymes do NOT change the energy of the starting point or the ending point of the reaction. They only lower the activation energy.

Enzyme Specificity

• Each enzyme catalyzes only one kind of reaction. This is known as enzyme specificity.

• Enzymes are usually named after the molecules they target. In enzymatic reactions, the targeted molecules are known as substrates.

Enzyme-Substrate Complex

• During a reaction, the enzyme’s job is to bring the transition state about by helping the substrate(s) get into position. It accomplishes this through a special region on the enzyme known as an active site.

• The enzyme temporarily binds one or more of the substrates to its active site and forms an enzyme-substrate complex.

• Enzymes Do: increase the rate of a reaction by lowering the reaction’s activation energy form temporary enzyme-substrate complexes remain unaffected by the reaction

• Enzymes Don’t: change the reaction make reactions occur that would otherwise not occur at all

Induced-fit

• Enzymes and substrates don’t fit together quite so seamlessly. Enzymes have to change its shape slightly to accommodate the shape of the substrates. This is called induced-fit.

• Because the fit between the enzyme and the substrate must be perfect, enzymes operate only under a strict set of biological conditions.

Enzymes Don’t Always Work Alone

• Enzymes sometimes need a little help in catalysing a reaction. Those factors are known as cofactors. Cofactors can be either organic molecules called coenzymes or inorganic molecules or ions.

• Inorganic cofactors are usually metal ions (Fe2+, Mg2+).

• Vitamins are examples of organic coenzymes

Factors Affecting Reaction Rates

• Enzymatic reactions can be influenced by a number of factors, such as temperature and pH. The concentrations of enzyme and substrate will also determine the speed of the reaction.

Temperature

• The rate of a reaction increases with increasing temperature.

• An increase in the temperature of a reaction increases the frequency of collisions among the molecules. But too much heat can damage an enzyme and becomes denatured.

• Enzyme denaturation is reversible if the original optimal environmental conditions of the enzyme are restored.

pH

• Enzymes also function best at a particular pH.

• At an incorrect pH, the hydrogen bonds can be disrupted and the structure of the enzyme can be altered

Relative Concentration of Substrates and Products

• The relative concentration of substrates and products can also affect the rate of an enzyme-catalysed reaction.

• An increase in substrate concentration will initially speed up the reaction. However, once all of the enzyme in solution is bound by substrate, the reaction can no longer speed up.

• This concentration of substrate where all of the enzyme in a reaction is bound by substrate is called the saturation point. Additional substrate past this point will no longer increase the speed of the reaction.

Enzyme Regulation

• A cell can control enzymatic activity by regulating the conditions that influence the shape of the enzyme.

• Enzymes can be turned on or off by things that bind to them. Sometimes these things can bind at the active site, and sometimes they bind at other sites, called allosteric sites.

• If the substance has a shape that fits the active site of an enzyme it can compete with the substrate and block the substrate from getting into the active site. This is called competitive inhibition. You can always identify a competitive inhibitor based on what happens when you flood the system with lots of substrate.

• If the inhibitor binds to an allosteric site, it is an allosteric inhibitor and it is noncompetitive inhibition. A noncompetitive inhibitor generally distorts the enzyme shape so that it cannot function. The substrate can still bind at the active site, but the enzyme will not be able to catalyze the reaction.

Reaction Coupling and ATP

• The cell gets its energy through adenosine triphosphate (ATP).

• ATP consists of a molecule of adenosine bonded to three phosphates. Enormous amount of energy is packed into those phosphate bonds.

• When a cell needs energy, it takes one of these potential-packed molecules of ATP and splits off the third phosphate, forming adenosine diphosphate (ADP) and one loose phosphate (Pi ), while releasing energy in the process. ATP → ADP + Pi + energy

• Organisms can use exergonic processes that increase energy, like breaking down ATP, to power endergonic reactions, like building organic macromolecules.

Sources of ATP

• ATP comes from a process called cellular respiration.

• Cellular respiration is a process of breaking down sugar and making ATP.

• In autotrophs, the sugar is made during photosynthesis.

• In heterotrophs, glucose comes from the food we eat.

Photosynthesis

• Photosynthesis is the process by which light energy is converted to chemical energy.

• 6CO2 + 6H2O C6H12O6 + 6O2

• You’ll notice from this equation that carbon dioxide and water are the raw materials used to manufacture simple sugars. Oxygen is one of the products of photosynthesis.

• There is strong evidence that prokaryotic photosynthesis contributed to the production of oxygen in the atmosphere. Furthermore, prokaryotic photosynthesis pathways laid the evolutionary foundation for eukaryotic photosynthesis to develop.

• There are two stages in photosynthesis: the light reactions (also called the light-dependent reactions) and the dark reactions (also called the light- independent reactions).

  • The whole process begins when photons (energy units) of sunlight strike a leaf, activating chlorophyll and exciting electrons.

  • The activated chlorophyll molecule then passes these excited electrons down to a series of electron carriers, ultimately producing ATP and NADPH.

  • Both of these products, along with carbon dioxide, are then used in the dark reactions (light-independent) to make carbohydrates.

  • Along the way, water is also split and oxygen gets released.

Chloroplast Structure

• The leaves of plants contain lots of chloroplasts, which are the primary sites of photosynthesis.

• If you split the membranes of a chloroplast, you’ll find a fluid-filled region called the stroma. Inside the stroma are structures that look like stacks of coins. These structures are the grana.

• The many disk-like structures that make up grana are called thylakoids. They contain chlorophyll, a light-absorbing pigment that drives photosynthesis, as well as enzymes involved in the process.

• The very inside of a thylakoid is called the thylakoid lumen.

• Many light-absorbing pigments participate in photosynthesis. Some of the more important ones are chlorophyll a, chlorophyll b, and carotenoids. These pigments are clustered in the thylakoid membrane into units called antenna complexes.

• All of the pigments within a unit are able to “gather” light, but they’re not able to “excite” electrons. The other pigments, called antenna pigments, “gather” light and “bounce” energy to the reaction center.

• There are two types of reaction centers:

  • photosystem I (PS I) and photosystem II (PS II). T

• The principal difference between the two is that each reaction center has a specific type of chlorophyll—chlorophyll a—that absorbs a particular wavelength of light.

• Autotrophs are using light and ADP and phosphates (that’s phosphorylation) to produce ATP. An absorption spectrum shows how well a certain pigment absorbs electromagnetic radiation. Light absorbed is plotted as a function of radiation wavelength. This spectrum is the opposite of an emission spectrum, which gives information on which wavelengths are emitted by a pigment.

• Carotenoids absorb light on the blue-green end of the spectrum, but not on the other end. This is why plants rich in carotenoids are yellow, orange, or red.

The Light Reactions

• When a leaf captures sunlight, the energy is sent to P680, the reaction center for photosystem II.

• The activated electrons are trapped by P680 and passed to a molecule called the primary acceptor, and then they are passed down to carriers in the electron transport chain.

• To replenish the electrons in the thylakoid, water is split into oxygen, hydrogen ions, and electrons. That process is called photolysis.

• The electrons from photolysis replace the missing electrons in photosystem II. As the energized electrons from photosystem II travel down the electron transport chain, they pump hydrogen ions into the thylakoid lumen. A proton gradient is established. As the hydrogen ions move back into the stroma through ATP synthase, ATP is produced.

• After the electrons leave photosystem II, they go to photosystem I. The electrons are passed through a second electron transport chain until they reach the final electron acceptor NADP+ to make NADPH. Photosystem I and photosystem II were numbered in order of their discovery, not the order they are used in photosynthesis.

The Light-Independent Reactions

• The dark reactions use the products of the light reactions—ATP and NADPH—to make sugar.

• We now have energy to make glucose, Their carbon source is CO2. Carbon fixation means is that CO2 from the air is converted into carbohydrates.

• This step occurs in the stroma of the leaf. The dark reactions are also called the Calvin-Benson Cycle

Plants that live in hot climates have evolved two different ways around this:

• CAM plants deal with this problem by temporally separating carbon fixation and the Calvin cycle.

• They open their stomata at night and incorporate CO2 into organic acids.

• During the day, they close their stomata and release CO2 from the organic acids while the light reactions run.

• In contrast, C4 plants have slightly different leaf anatomy that allows them to perform CO2 fixation in a different part of the leaf from the rest of the Calvin cycle. This prevents photorespiration.

• C4 plants produce a four- carbon molecule as the first product of carbon fixation and perform cyclic electron flow in the light reactions.

Cellular Respiration

• C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

• You can break cellular respiration down into two different approaches:

• aerobic respiration and anaerobic respiration.

• If ATP is made in the presence of oxygen, we call it aerobic respiration. If oxygen

• If it isn’t present, we call it anaerobic respiration.

Introduction to Aerobic Respiration

Aerobic respiration consists of four stages containing a series of coupled reactions that establish an electrochemical gradient across membranes:

1. glycolysis

2. formation of acetyl-CoA

3. the Krebs (citric acid) cycle

4. oxidative phosphorylation (the electron transport chain + chemiosmosis)

Stage 1: Glycolysis

• The first stage begins with glycolysis, the splitting of glucose

  • Glucose is a six-carbon molecule that is broken into two three- carbon molecules called pyruvic acid.

  • This breakdown of glucose also results in the net production of two molecules of ATP and two molecules of NADH.

  • Glucose + 2 ATP + 2NAD+ → 2 Pyruvic acid + 4 ATP + 2NADH

  • Glycolysis also creates two NADH, which result from the transfer of electrons to the carrier NAD+, which then becomes NADH.

  • NAD+ and NADH are constantly being turned into each other as electrons are being carried and then unloaded.

There are four important tidbits to remember regarding glycolysis:

• occurs in the cytoplasm

• net of 2 ATPs produced

• 2 pyruvic acids formed

• 2 NADH produced

Stage 2: Formation of Acetyl-CoA

• Pyruvic acid is transported to the mitochondrion.

• Each pyruvic acid (a three-carbon molecule) is converted to acetyl-coenzyme

• A (a two-carbon molecule, usually just called acetyl-CoA) and CO2 is released.

• 2 Pyruvic acid + 2 Coenzyme A + 2NAD+ → 2 Acetyl-CoA + 2CO2 + 2NADH

• From two 3- carbon molecules to now two 2-carbon molecules.

• The extra carbons leave the cell in the form of CO2. Once again, two molecules of NADH are also produced for each glucose you started with.

• This process of turning pyruvic acid into acetyl-CoA is catalyzed by an enzyme complex called the pyruvate dehydrogenase complex (PDC).

Stage 3: The Krebs Cycle

• Also known as the citric acid cycle.

  • The Krebs cycle begins with each molecule of acetyl-CoA produced from the second stage of aerobic respiration combining with oxaloacetate, a four-carbon molecule, to form a six-carbon molecule, citric acid or citrate.

  • In the mitochondria, pyruvate is turned into acetyl- CoA and 1 NADH is made; double this if you are counting per glucose.

  • The Krebs cycle occurs in the mitochondrial matrix.

  • It begins with acetyl-CoA joining with oxaloacetate to make citric acid and ends with oxaloacetate, 1 ATP, 3 NADH, and 1 FADH2; double this if you are counting per glucose.

  • Citrate gets turned into several other things, and because the cycle begins with a four-carbon molecule, oxaloacetate, it eventually gets turned back into oxaloacetate to maintain the cycle by joining with the next acetyl-CoA coming down the pipeline.

• With each turn of the cycle, three types of energy are produced:

  • 1 ATP

  • 3 NADH

  • 1 FADH2

• To figure out the total number of products per molecule of glucose, we simply double the number of products.

Stage 4: Oxidative Phosphorylation

Electron Transport Chain

• As electrons are removed from a molecule of glucose, they carry much energy that was originally stored in their chemical bonds.

• These electrons are transferred to readied hydrogen carrier molecules.

• In the case of cellular respiration, these charged carriers are the coenzymes NADH and FADH2.

• We now have:

  • 2 NADH molecules from glycolysis

  • 2 NADH from the production of acetyl-CoA

  • 6 NADH from the Krebs cycle

  • 2 FADH2 from the Krebs cycle

• That gives us a total of 12 electron or energy carriers altogether.

• These electron carriers—NADH and FADH2—“shuttle” electrons to the electron transport chain, the resulting NAD+ and FADH can be recycled to be used as carriers again, and the hydrogen atoms are split into hydrogen ions and electrons.

• The high-energy electrons from NADH and FADH2 are passed down a series of protein carrier molecules that are embedded in the cristae; thus, it is called the electron transport chain.

• Some of the carrier molecules in the electron transport chain are NADH dehydrogenase and cytochrome C.

• Each carrier molecule hands down the electrons to the next molecule in the chain.

• The electrons travel down the electron transport chain until they reach the final electron acceptor, oxygen. Oxygen combines with these electrons (and some hydrogens) to form water.

• This explains the “aerobic” in aerobic respiration. If oxygen weren’t available to accept the electrons, they wouldn’t move down the chain at all, thereby shutting down the whole process of electron transport.

Chemiosmosis

• The energy released from the electron transport chain is used to pump hydrogen ions across the inner mitochondrial membrane from the matrix into the inter-membrane space.

• The pumping of hydrogen ions into the inter-membrane space creates a pH gradient, or proton gradient.

• The hydrogen ions really want to diffuse back into the matrix. The potential energy established in this gradient is responsible for the production of ATP.

• This pumping of ions and diffusion of ions to create ATP is chemiosmosis

• Overall, this process is called oxidative phosphorylation because when electrons are given up it is called “oxidation” and then ADP is “phosphorylated” to make ATP.

• You’re also expected to know the following two things for the AP Biology Exam:

• Every NADH from glycolysis yields 1.5 ATP and all other NADH molecules yield 2.5 ATP.

• Every FADH2 yields 1.5 ATP.

You will also want to make sure you remember the major steps of cell respiration, and the outcome of each steM

Photosynthesis vs. Cell Respiration

• In both cases, ATP production is driven by a proton gradient, and the proton gradient is created by an electron transport chain.

• In respiration, protons are pumped from the mitochondrial matrix to the intermembrane space, and they return to the matrix through an ATP synthase down their concentration gradient.

• In photosynthesis, protons are pumped from the stroma into the thylakoids compartment, and they return to the stroma through an ATP synthase down their concentration gradient.

• The Krebs cycle seeks to oxidize carbohydrates to CO2, while the Calvin cycle seeks to reduce CO2 to carbohydrates.

Anaerobic Respiration

• When oxygen is not available, the anaerobic version of respiration occurs.

  • The electron transport chain stops working, and electron carriers have nowhere to drop their electrons.

  • The mitochondrial production of acetyl- CoA and the Krebs cycle cease too.

  • Glycolysis, however, can continue to run. This means that glucose can be broken down to give net two ATP. Only two instead of 30!

  • Glycolysis also gives two pyruvates and two NADH. The pyruvate and NADH make a deal with each other, and pyruvate helps NADH get recycled back into NAD+ and takes its electrons.

  • The pyruvate turns into either lactic acid (in muscles) or ethanol (in yeast).

  • Since these two things are toxic at high concentrations, this process, called fermentation, is done only in emergencies. Aerobic respiration is a better option

• What types of organisms undergo fermentation?

  • Yeast cells and some bacteria make ethanol and carbon dioxide. Other bacteria produce lactic acid.

Your Muscle Cells Can Ferment

• A cramp was possibly the consequence of anaerobic respiration.

• When you exercise, your muscles require a lot of energy.

• To get this energy, they convert enormous amounts of glucose to ATP.

• As you continue to exercise, your body doesn’t get enough oxygen to keep up with the demand in your muscles. This creates an oxygen debt.

• Muscles switch over to anaerobic respiration.

• Pyruvic acid produced from glycolysis is converted to lactic acid.

Unit 4: Cell Communication and Cell Cycle

Cell Communication

• Unicellular organisms detect and respond to environmental signals.

• Taxis is the movement of an organism in response to a stimulus and can be positive (toward the stimulus) or negative (away from the stimulus).

• Taxes are innate behavioral responses, or instincts. Chemotaxis is movement in response to chemicals.

Signal Transduction & Changes In Pathways

• The cells of multi-celled organisms must communicate with one another to coordinate the activities of the organism as a whole.

• Cells communicate through cell-to-cell contact or through cell signaling. Signaling can be short-range (affecting only nearby cells) or long-range (affecting cells throughout the organism).

• It can be done by cell junctions or signalling molecules called ligands that bind to receptors and trigger a response by changing the shape of the receptor protein.

• Signal transduction is the process by which an external signal is transmitted to the inside of a cell. It usually involves the following three steps:

  1. a signaling molecule binding to a specific receptor

  2. activation of a signal transduction pathway

  3. production of a cellular response

• For signaling molecules that cannot enter the cell, a plasma membrane receptor is required.

• Plasma membrane receptors form an important class of integral membrane proteins that transmit signals from the extracellular space into the cytoplasm. Each receptor binds a particular molecule in a highly specific way.

There are three classes of membrane receptors.

1. Ligand-gated ion channels in the plasma membrane open or close an ion channel upon binding a particular ligand. This channel opens in response to acetylcholine, and a massive influx of sodium depolarises the muscle cell and causes it to contract.

2. Catalytic (enzyme-linked) receptors have an enzymatic active site on the cytoplasmic side of the membrane. Enzyme activity is initiated by ligand binding at the extracellular surface.

3. A G-protein-linked receptor does not act as an enzyme, but instead will bind a different version of a G-protein (often GTP or GDP) on the intracellular side when a ligand is bound extracellularly. This causes activation of secondary messengers within the cell. One important second messenger is cyclic AMP (cAMP).

• Signal transduction cascades are helpful to amplify a signal.

FEEDBACK

• The set of conditions under which living things can successfully survive is called homeostasis.

• Your blood glucose levels are regulated by insulin and glucagon, two hormones released from your pancreas.

• Many of these responses are controlled by negative or positive feedback pathways.

• A negative feedback pathway (also called feedback inhibition) works by turning itself off using the end product of the pathway. The end product inhibits the process from beginning, thus shutting down the pathway.

A positive feedback pathway also involves an end product playing a role, but instead of inhibiting the pathway, it further stimulates it.

The cell cycle

• Every cell has a life cycle—the period from the beginning of one division to the beginning of the next.

• The cell’s life cycle is known as the cell cycle.

• The cell cycle is divided into two periods: interphase and mitosis.

Interphase: the growing phase

• Interphase is the time span from one cell division to another.

• The Three Stages of Interphase Interphase can be divided into three stages: G1, S, G2.

• The most important phase is the S phase. That’s when the cell replicates its genetic material.

• During interphase, every single chromosome in the nucleus is duplicated.

• These identical strands of DNA are now called sister chromatids.

• The chromatids are held together by a structure called the centromere.

• You can think of each chromatid as a chromosome, but because they remain attached, they are called chromatids instead.

• To be called a chromosome, each needs to have its own centromere.

• Once the chromatids separate, they will be full-fledged chromosomes.

Cell Cycle Regulation

• G1 and G2- During these stages, the cell performs metabolic reactions and produces organelles, proteins, and enzymes.

• G stands for “gap,” but we can also associate it with “growth.”

• These three phases are highly regulated by checkpoints and special proteins called cyclins and cyclin-dependent kinases (CDKs).

• Cell cycle checkpoints are control mechanisms that make sure cell division is happening properly in eukaryotic cells.

• In eukaryotes, checkpoint pathways function mainly at phase boundaries (such as the G1/S transition and the G2/M transition).

• When damaged DNA is found, checkpoints are activated and cell cycle progression stops. The cell uses the extra time to repair damage in DNA. If the DNA damage is so extensive that it cannot be repaired, the cell can undergo apoptosis, or programmed cell death.

• Cell cycle checkpoints control cell cycle progression by regulating two families of proteins:

  • cyclin-dependent kinases (CDKs)

  • cyclins.

• To induce cell cycle progression, an inactive CDK binds a regulatory cyclin. Once together, the complex is activated, can affect many proteins in the cell, and causes the cell cycle to continue.

• To inhibit cell cycle progression, CDKs and cyclins are kept separate. CDKs and cyclins were first studied in yeast, unicellular eukaryotic fungi.

Cancer

• Cancer occurs when normal cells start behaving and growing very abnormally and spread to other parts of the body.

• Mutated genes that induce cancer are called oncogenes.

• They are genes that can convert normal cells into cancerous cell healthy version is called a proto-oncogene.

• Tumour suppressor genes produce proteins that prevent the conversion of normal cells into cancer cells. They can detect damage to the cell and work with CDK/cyclin complexes to stop cell growth until the damage can be repaired.

• They can also trigger apoptosis if the damage is too severe to be repaired.

Mitosis: the dance of the chromosomes

• Mitosis, or cellular division, occurs in four stages:

• prophase, metaphase, anaphase, and telophase.

• During prophase, the nuclear envelope disappears and chromosomes condense.

• Next is metaphase, when chromosomes align at the metaphase plate and mitotic spindles attach to kinetochores.

• In anaphase, chromosomes are pulled away from the center. Telophase terminates mitosis, and the two new nuclei form.

• The process of cytokinesis, which occurs during telophase, ends mitosis, as the cytoplasm and plasma membranes pinch to form two distinct, identical daughter cells.

• Interphase Once daughter cells are produced, they reenter the initial phase—interphase —and the whole process starts over. The cell goes back to its original state. Once again, the chromosomes decondense and become invisible, and the genetic material is called chromatin again.

Purpose of Mitosis

• Mitosis achieves two things:

• The production of daughter cells that are identical copies of the parent cell maintaining the proper number of chromosomes from generation to generation

• The impetus to divide occurs because an organism needs to grow, a tissue needs repair, or asexual reproduction must take place.

• ked.

• In a pedigree chart, the males are squares and the females are circles.

Environmental Effect on Traits

• Changes in genotypes can result in changes in phenotype, but environmental factors also influence many traits, directly and indirectly.

• Furthermore, an organism’s adaptation to the local environment reflects a flexible response of its genome

• Phenotypic plasticity occurs if two individuals with the same genotype have different phenotypes since they are in different environments.

An Overview of Meiosis

• Meiosis is the production of gametes.

• Meiosis is limited to sex cells in special sex organs called gonads.

• In males, the gonads are the testes, while in females they are the ovaries.

• The special cells in these organs—also known as germ cells—produce haploid cells (n), and they combine to restore the diploid (2n) number during fertilization. female gamete (n) + male gamete (n) = zygote (2n)

Meiosis is likely to produce sorts of variations than is mitosis, which therefore confers selective advantage on sexually reproducing organisms.

A Closer Look at Meiosis

• Meiosis actually involves two rounds of cell division: meiosis I and meiosis II.

• Before meiosis begins, the diploid cell goes through interphase. Just as in mitosis, double-stranded chromosomes are formed during S phase.

• Meiosis I

  • Meiosis I consists of four stages: prophase I, metaphase I, anaphase I, and telophase I.

  • Meiosis I ensures that each gamete receives a haploid (1n) set of chromosomes.

• Prophase I

  • As in mitosis, the nuclear membrane disappears, the chromosomes become visible, and the centrioles move to opposite poles of the nucleus.

  • The major difference involves the movement of the chromosomes. In meiosis, the chromosomes line up side-by-side with their counterparts (homologs). This event is known as synapsis.

  • Synapsis involves two sets of chromosomes that come together to form a tetrad (a bivalent). A tetrad consists of four chromatids. Synapsis is followed by crossing-over, the exchange of segments between homologous chromosomes.

  • What’s unique in prophase I is that pieces of chromosomes are exchanged between homologous partners. This is one of the ways organisms produce genetic variation.

• Metaphase I

  • As in mitosis, the chromosome pairs—now called tetrads—line up at the metaphase plate.

  • By contrast, you’ll recall that in regular metaphase, the chromosomes line up individually.

  • One important concept to note is that the alignment during metaphase is random, so the copy of each chromosome that ends up in a daughter cell is random.

• Anaphase I

  • During anaphase I, each pair of chromatids within a tetrad moves to opposite poles. The homologs will separate with their centromeres intact.

  • The chromosomes now move to their respective poles.

• Telophase I

• During telophase I, the nuclear membrane forms around each set of chromosomes.

• Finally, the cells undergo cytokinesis, leaving us with two daughter cells.

• Meiosis II

  • The purpose of the second meiotic division is to separate sister chromatids

• During prophase II, chromosomes once again condense and become visible.

• In metaphase II, chromosomes move toward the metaphase plate. This time they line up single file, not as pairs.

• During anaphase II, chromatids of each chromosome split at the centromere, and each chromatid is pulled to opposite ends of the cell.

• At telophase II, a nuclear membrane forms around each set of chromosomes and a total of four haploid cells are produced.

Gametogenesis

• Meiosis is also known as gametogenesis.

• If sperm cells are produced, then meiosis is called spermatogenesis.

• During spermatogenesis, four sperm cells are produced for each diploid cell.

• If an egg cell or an ovum is produced, this process is called oogenesis.

• Oogenesis produces only one ovum, not four. The other three cells, called polar bodies, get only a tiny amount of cytoplasm and eventually degenerate since the female wants to conserve as much cytoplasm as possible for the surviving gamete, the ovum.

Meiotic Errors

• Nondisjunction—chromosomes failed to separate properly during meiosis.

• This error, which produces the wrong number of chromosomes in a cell, usually results in miscarriage or significant genetic defects.

• Individuals with Down syndrome have three—instead of two—copies of the 21st chromosome.

• Nondisjunction can occur in **anaphase I (**meaning chromosomes don’t separate when they should), or in anaphase II (meaning chromatids don’t separate).

• Either one can lead to aneuploidy, or the presence of an abnormal number of chromosomes.