Chemistry Chapter: Atoms and Bonds
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Questions and Answers

What is the primary function of P680 in Photosystem II?

  • To absorb light at a wavelength of 700 nm
  • To act as the primary electron donor to the electron transport chain
  • To absorb light at a wavelength of 680 nm (correct)
  • To reduce NADP+ to NADPH
  • Which of the following statements accurately describes linear electron flow?

  • It involves both Photosystem I and II and produces both ATP and NADPH. (correct)
  • It is a process that occurs during the Calvin cycle.
  • It can result in the production of NADPH and does not involve water splitting.
  • It solely relies on Photosystem I to produce ATP.
  • How is P680+ generated in the light reactions?

  • Through the transfer of electrons from P680 to the primary electron acceptor (correct)
  • By the splitting of water molecules releasing oxygen
  • By the absorption of a photon by P700
  • When NADP+ is reduced to form NADPH
  • What distinguishes cyclic electron flow from linear electron flow?

    <p>Cyclic flow does not involve Photosystem II, while linear flow does. (A)</p> Signup and view all the answers

    What role do the electrons from water play in the light reactions of photosynthesis?

    <p>They are transferred to P680+, helping to reduce it back to P680. (D)</p> Signup and view all the answers

    What is the primary function of Photosystem II during the light reactions of photosynthesis?

    <p>To split H2O and release O2 (D)</p> Signup and view all the answers

    Which structure is primarily involved in the generation of ATP during photophosphorylation?

    <p>Thylakoid membranes (A)</p> Signup and view all the answers

    What distinguishes linear electron flow from cyclic electron flow in photosynthesis?

    <p>Linear flow produces NADPH and ATP, while cyclic flow produces only ATP. (B)</p> Signup and view all the answers

    Which element of the electron transport chain contributes to the creation of a proton gradient across the thylakoid membrane?

    <p>Light energy (C)</p> Signup and view all the answers

    During the Calvin cycle, what is the main use of the ATP and NADPH generated in the light reactions?

    <p>To convert CO2 into sugar (C)</p> Signup and view all the answers

    What is a key characteristic of Photosystem II (PS II)?

    <p>It initiates the process of photophosphorylation. (C)</p> Signup and view all the answers

    Which components are involved in the structure of a photosystem?

    <p>A reaction-center complex and a light-harvesting complex. (A)</p> Signup and view all the answers

    How do the light-harvesting complexes contribute to photosynthesis?

    <p>They transfer energy from photons to chlorophyll a molecules. (D)</p> Signup and view all the answers

    What drives the linear electron flow in the photosystems?

    <p>Excitement of electrons from chlorophyll a to the primary electron acceptor. (D)</p> Signup and view all the answers

    What is the purpose of the electron transport chain within the light reactions?

    <p>To generate ATP and NADPH for the Calvin Cycle. (B)</p> Signup and view all the answers

    Which statement correctly describes cyclic electron flow?

    <p>It funnels electrons back to chlorophyll a in Photosystem I. (C)</p> Signup and view all the answers

    During photophosphorylation, what is the primary energy source used?

    <p>The energy derived from electron movement in the thylakoid membrane. (A)</p> Signup and view all the answers

    What is the main function of accessory pigments like carotenoids?

    <p>To absorb excessive light that could damage chlorophyll. (A)</p> Signup and view all the answers

    What happens when a chlorophyll molecule absorbs light?

    <p>It transitions to an excited state and may release energy as heat or fluorescence. (B)</p> Signup and view all the answers

    What distinguishes the absorption spectrum of chlorophyll a from that of chlorophyll b?

    <p>They have slight structural differences affecting their absorption capacities. (B)</p> Signup and view all the answers

    What happens to the free energy of a system during a spontaneous change?

    <p>It decreases, resulting in increased stability. (A)</p> Signup and view all the answers

    What characterizes a system in equilibrium?

    <p>It experiences a stable condition with no net change. (B)</p> Signup and view all the answers

    Which statement accurately reflects the concept of entropy?

    <p>Entropy is a measure of molecular disorder or randomness. (B)</p> Signup and view all the answers

    How do catabolic pathways generally influence free energy in a system?

    <p>They decrease free energy by breaking down complex molecules. (D)</p> Signup and view all the answers

    What is a defining feature of living cells regarding their metabolic state?

    <p>Cells are open systems with a constant flow of materials. (B)</p> Signup and view all the answers

    What is the primary role of enzymes in metabolic reactions?

    <p>To lower energy barriers for reactions (C)</p> Signup and view all the answers

    Which statement correctly describes sucrase's function?

    <p>It hydrolyzes sucrose into glucose and fructose. (C)</p> Signup and view all the answers

    How does ATP contribute to cellular work?

    <p>By transferring energy through phosphorylation of ADP (C)</p> Signup and view all the answers

    What is the result of hydrolysis of the phosphate bonds in ATP?

    <p>It converts ATP into ADP and releases inorganic phosphate. (D)</p> Signup and view all the answers

    In which type of reactions is ATP primarily used?

    <p>In both catabolic and anabolic processes (B)</p> Signup and view all the answers

    What is the effect of an allosteric activator on an enzyme?

    <p>It stabilizes the active form of the enzyme. (D)</p> Signup and view all the answers

    What is the primary purpose of feedback inhibition in metabolic pathways?

    <p>To conserve cellular resources by shutting down pathways when enough product is produced. (C)</p> Signup and view all the answers

    How does cooperativity differ from other forms of allosteric regulation?

    <p>It amplifies enzyme activity upon binding of a substrate to one active site. (C)</p> Signup and view all the answers

    What role do structural compartments within a cell play in metabolism?

    <p>They help localize enzymes to specific organelles for metabolic efficiency. (B)</p> Signup and view all the answers

    Which statement best describes how allosteric regulation operates?

    <p>It involves the binding of molecules at one site influencing activity at another site. (C)</p> Signup and view all the answers

    What happens to the metabolic pathway when isoleucine binds to the allosteric site of threonine deaminase?

    <p>The active site becomes unavailable, halting the pathway. (B)</p> Signup and view all the answers

    Why are most allosterically regulated enzymes constructed from polypeptide subunits?

    <p>It facilitates the active and inactive forms of the enzyme. (B)</p> Signup and view all the answers

    What is the effect of an inhibitor on an allosteric enzyme?

    <p>It stabilizes the inactive form of the enzyme. (A)</p> Signup and view all the answers

    What type of protein extends across the membrane and is integral to its function?

    <p>Transmembrane protein (A)</p> Signup and view all the answers

    Which of the following interactions primarily holds the lipid bilayer together?

    <p>Hydrophobic interactions (D)</p> Signup and view all the answers

    Which cellular function is NOT attributed to membrane proteins?

    <p>DNA replication (A)</p> Signup and view all the answers

    Which feature of the fluid mosaic model emphasizes the movement of lipids and proteins within the membrane?

    <p>Lateral movement of lipids and some proteins (A)</p> Signup and view all the answers

    What type of amino acids are predominantly found in the hydrophobic regions of integral proteins?

    <p>Nonpolar amino acids (B)</p> Signup and view all the answers

    Which of the following terms describes proteins that are bound to the membrane surface rather than penetrating it?

    <p>Peripheral proteins (A)</p> Signup and view all the answers

    What was the main purpose of the heterokaryon experiments in cell membrane studies?

    <p>To illustrate the fluidity of membranes (D)</p> Signup and view all the answers

    Which of the following is NOT a function of membrane proteins?

    <p>Nutrient storage (C)</p> Signup and view all the answers

    What hormone is produced by adipose tissue and plays a role in suppressing appetite?

    <p>Leptin (D)</p> Signup and view all the answers

    Which structure in the small intestine greatly increases the rate of nutrient absorption?

    <p>Microvilli (D)</p> Signup and view all the answers

    When glycogen stores are full, where does the excess energy get stored in the body?

    <p>As triglycerides in adipose cells (A)</p> Signup and view all the answers

    During the non-fasting state, what triggers released insulin to assist with glucose uptake in cells?

    <p>Increase in blood glucose levels (D)</p> Signup and view all the answers

    Which statement accurately describes how amino acids in excess of the body's needs are processed?

    <p>They are turned into keto acids and urea. (A)</p> Signup and view all the answers

    What is the first form of energy storage in the human body when excess energy is not immediately needed?

    <p>Glycogen in liver and muscle cells (A)</p> Signup and view all the answers

    Which pathway do fats undergo to be used as an energy source?

    <p>B-oxidation in mitochondria (A)</p> Signup and view all the answers

    What is the primary role of leptin in body regulation?

    <p>Regulating body fat levels and suppressing appetite (B)</p> Signup and view all the answers

    Which of the following steps in glycolysis is exergonic and cannot be reversed?

    <p>Step 1 (D)</p> Signup and view all the answers

    What is the consequence of high levels of ADP and glucose in gluconeogenesis?

    <p>They inhibit pyruvate carboxylase activity. (A)</p> Signup and view all the answers

    What enzyme is responsible for converting fructose 1,6-bisphosphate (F1,6BP) to fructose 6-phosphate (F6P) in gluconeogenesis?

    <p>Fructose bisphosphatase (A)</p> Signup and view all the answers

    What molecule is used in gluconeogenesis to export oxaloacetate from the mitochondria to the cytosol?

    <p>Malate (A)</p> Signup and view all the answers

    Which of the following correctly describes the mechanism by which glucose-6-phosphate is converted to glucose?

    <p>It is hydrolyzed by glucose-6-phosphatase. (A)</p> Signup and view all the answers

    What role does GTP play in the conversion of oxaloacetate to phosphoenolpyruvate?

    <p>It is hydrolyzed to GDP. (C)</p> Signup and view all the answers

    What is the main regulatory role of fructose 2,6-bisphosphate (F2,6BP) in gluconeogenesis?

    <p>It inhibits fructose bisphosphatase. (D)</p> Signup and view all the answers

    What is the primary reason glucose-6-phosphate is retained in the cell?

    <p>It is phosphorylated and cannot diffuse out of the cell. (A)</p> Signup and view all the answers

    Flashcards

    P680

    The reaction-center chlorophyll a in Photosystem II (PS II).

    P700

    The reaction-center chlorophyll a in Photosystem I (PS I).

    Linear electron flow

    The primary pathway of light-dependent reactions in photosynthesis, involving both PSII and PSI, producing ATP and NADPH.

    Photosystem II (PS II)

    The first photosystem in the light-dependent reactions of photosynthesis.

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    Water splitting

    The process where water is broken down to provide electrons and H+ ions in PS II.

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    Light Reactions

    The first stage of photosynthesis, occurring in the thylakoid membranes, where light energy is converted to chemical energy in the form of ATP and NADPH, while splitting water and releasing oxygen.

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    Calvin Cycle

    The second stage of photosynthesis, which takes place in the stroma of the chloroplast, where Carbon Dioxide is fixed to create sugars using ATP and NADPH generated from light reactions.

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    Photosynthesis

    The process by which plants and some other organisms use the energy of sunlight to convert water and carbon dioxide into sugar (glucose), releasing oxygen as a byproduct.

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    Chloroplast

    The organelle in plant cells where photosynthesis takes place. It has thylakoids and stroma.

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    Wavelength

    The distance between successive crests of a wave, such as light waves.

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    Chlorophyll a

    A primary pigment in photosynthesis, absorbing light mainly in the red and blue regions of the spectrum.

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    Photosynthesis action spectrum

    Shows the efficiency of different wavelengths of light for driving photosynthesis.

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    Accessory pigments

    Pigments like chlorophyll b and carotenoids that absorb light at different wavelengths than chlorophyll a, expanding the range of light used by plants for photosynthesis.

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    Photosystem

    A complex of proteins and pigments that capture light energy and convert it into chemical energy.

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    Reaction-center complex

    Part of a photosystem containing chlorophyll a molecules that directly convert light energy into chemical energy, beginning the light reactions (transfer electrons).

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    Light-harvesting complexes

    Pigments that capture light energy and move it to the reaction-center complex in a photosystem.

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    Excited state

    The unstable condition of a pigment molecule after absorbing a photon of light.

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    Fluorescence

    The emission of light by a molecule when it loses energy by releasing a photon after returning to the ground state from an excited state.

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    Carotenoids

    Accessory pigments that absorb light in the blue-green and yellow-orange parts of the spectrum; protect chlorophyll from excessive light.

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    Entropy

    A measure of molecular disorder or randomness within a system. Higher entropy means greater disorder.

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    Second Law of Thermodynamics

    States that every energy transfer or transformation increases the entropy of the universe. In other words, disorder always increases over time.

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    Free Energy

    A measure of a system's instability or tendency to change into a more stable state. Higher free energy means greater instability.

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    Spontaneous Change

    A process that occurs without outside intervention. In a spontaneous change, free energy decreases, and the system becomes more stable.

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    Equilibrium

    A state of maximum stability where there is no net change in free energy. A system at equilibrium cannot perform work.

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    Enzyme's Role in Reaction Rate

    Enzymes accelerate metabolic reactions by lowering the activation energy (EA) barrier, but they do not affect the change in free energy (ΔG).

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    Activation Energy (EA)

    The initial energy input required to start a chemical reaction, even if it is exergonic (releases energy overall).

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    How do enzymes lower EA?

    Enzymes lower EA by:

    1. Orienting substrates correctly for interaction
    2. Straining substrate bonds to make them easier to break
    3. Providing a favorable microenvironment for the reaction.
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    What is ATP?

    Adenosine triphosphate (ATP) is the cell's energy currency, a molecule that readily releases energy when its phosphate bonds break.

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    ATP Cycle

    The continuous regeneration of ATP from ADP (adenosine diphosphate) using energy derived from catabolic processes (energy-releasing reactions), and then ATP is used to power anabolic processes (energy-consuming reactions).

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    Allosteric Regulation

    A process where a regulatory molecule binds to a protein at a site separate from the active site, affecting the protein's function.

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    Feedback Inhibition

    A mechanism where the end product of a metabolic pathway inhibits an earlier step in the pathway, preventing overproduction.

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    How does feedback inhibition work?

    The end product of a metabolic pathway binds to an allosteric site on an enzyme, changing its shape and inhibiting its activity.

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    Cooperativity

    A type of allosteric activation where the binding of one substrate molecule to an enzyme enhances the binding of subsequent substrate molecules.

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    How does cooperativity work?

    The binding of a substrate to one active site on a multi-subunit enzyme causes conformational changes, making other active sites more likely to bind to the substrate.

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    Localization of enzymes

    Enzymes are often located in specific compartments within cells, allowing for organized metabolic pathways.

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    Example: Mitochondrial Enzymes

    Enzymes involved in cellular respiration are located in mitochondria, a specific organelle within eukaryotic cells.

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    Structural Enzymes

    Some enzymes act as structural components of membranes, contributing to their function.

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    Lipid Composition

    The types and amounts of lipids found in a cell membrane. These vary based on the environment the cell lives in. For example, cells in cold environments have more unsaturated lipids to maintain fluidity.

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    Integral Membrane Proteins

    Proteins that are embedded within the phospholipid bilayer of a cell membrane. They have hydrophobic regions that interact with the membrane's interior and hydrophilic regions that interact with the aqueous environments outside and inside the cell.

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    Transmembrane Protein

    A type of integral membrane protein that spans the entire width of the cell membrane, with portions exposed on both the extracellular and cytoplasmic sides.

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    Fluid Mosaic Model

    The current model of cell membrane structure, describing the membrane as a dynamic and fluid structure with phospholipids forming a bilayer and proteins embedded within it like a mosaic.

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    Membrane Fluidity

    The ability of the cell membrane to change its shape and move its components within the membrane. This is essential for cell function.

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    Heterokaryon Experiments

    Experiments that fuse cells from different species to demonstrate the fluidity of the plasma membrane. The experiment showed that membrane proteins from different species could mix within the hybrid cell's membrane.

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    Functions of Membrane Proteins

    Membrane proteins play crucial roles in various cellular processes, including transport, enzymatic activity, cell signaling, cell-cell recognition, and attachment to the cytoskeleton and extracellular matrix.

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    Cell-Cell Recognition

    The process by which cells recognize and interact with each other, often mediated by specific membrane proteins.

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    Leptin

    A hormone produced by fat cells that signals the brain to suppress appetite and reduce food intake, helping regulate body fat levels.

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    Ghrelin

    A hormone produced mainly in the stomach that stimulates appetite and increases food intake. It is often referred to as the 'hunger hormone'.

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    What is the main function of villi and microvilli in the small intestine?

    To increase the surface area of the small intestine, maximizing nutrient absorption from food.

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    How do nutrients get from the small intestine into the bloodstream?

    Nutrients are absorbed through epithelial cells lining the small intestine, either passively (following concentration gradients) or actively (requiring energy).

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    How does the body store excess energy?

    Excess energy is first stored as glycogen in the liver and muscle cells. When glycogen storage is full, excess energy is stored as triglycerides (fats) in adipose cells.

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    What happens to carbohydrates during the 'non-fasting' state?

    Carbohydrates are broken down into glucose. Some is used immediately, but most goes into the bloodstream, triggering insulin release and uptake of glucose by cells. Excess glucose is stored as glycogen.

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    What happens to fats during the 'non-fasting' state?

    Fats are digested and packaged into lipoproteins. Excess fat is stored as triglycerides. When used as energy, fats are broken down in mitochondria through beta-oxidation.

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    What happens to proteins during the 'non-fasting' state?

    Proteins are broken down into amino acids, used for building new proteins or entering the amino acid pool. Excess amino acids are converted into keto acids and urea, which are used for energy or excreted.

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    Gluconeogenesis

    The metabolic process of synthesizing glucose from non-carbohydrate sources, such as pyruvate, lactate, glycerol, and amino acids.

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    Pyruvate Carboxylase

    An enzyme that catalyzes the carboxylation of pyruvate to oxaloacetate, a crucial step in gluconeogenesis.

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    PEPCK

    Phosphoenolpyruvate carboxykinase, an enzyme that catalyzes the decarboxylation and phosphorylation of oxaloacetate to phosphoenolpyruvate, another crucial step in gluconeogenesis.

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    Fructose 1,6-Bisphosphatase

    An enzyme responsible for the conversion of fructose 1,6-bisphosphate (F1,6BP) to fructose 6-phosphate (F6P), a key step in gluconeogenesis.

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    Rate-limiting step of gluconeogenesis

    The conversion of fructose 6-phosphate to fructose 1,6-bisphosphate, catalyzed by phosphofructokinase 1, is the rate-limiting step of gluconeogenesis.

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    Glucose-6-phosphatase

    An enzyme that catalyzes the hydrolysis of glucose-6-phosphate to glucose and inorganic phosphate in the endoplasmic reticulum, the final step of gluconeogenesis.

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    Regulation of Gluconeogenesis

    Gluconeogenesis is regulated by various factors, including the availability of substrates, hormones like glucagon and insulin, and the energy state of the cell.

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    Difference from Glycolysis

    While glycolysis is the breakdown of glucose, gluconeogenesis is the synthesis of glucose. They share some reversible steps, but gluconeogenesis has unique irreversible steps catalyzed by different enzymes.

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    Study Notes

    Molecules to Cells

    • All matter in the universe is composed of atoms
    • Atoms are composed of subatomic particles, including neutrons, protons, and electrons
    • Neutrons and protons form the atomic nucleus, which has an almost identical mass
    • Electrons form a cloud of negative charge around the nucleus

    Periodic Table

    • The periodic table shows the electron distribution for each element
    • Valence electrons (those in the outermost shell) determine an atom's chemical behavior
    • Elements with a full valence shell are chemically inert

    Chemical Bonds

    • Ionic interactions involve the transfer of valence electrons, creating charged atoms (ions)
    • Covalent bonds involve the sharing of valence electrons
    • A single covalent bond is the sharing of one pair of valence electrons
    • A double covalent bond is the sharing of two pairs of valence electrons
    • Hydrogen bonds are weak attractions between a hydrogen atom and another electronegative atom.

    Weak Interactions

    • Hydrogen bonds and van der Waals interactions are weak interactions that hold large molecules in their functional form.
    • In hydrogen bonds, a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom.

    The Elements of Life

    • About 20-25% of the 92 natural elements are essential for life
    • Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter

    Biological Organization

    • Life can be studied at many levels, from molecules to the entire living planet
    • Emergent properties arise from complex interactions at different levels.

    The Molecules of Life

    • Large biological molecules: carbohydrates, lipids, proteins, and nucleic acids
    • Macromolecules are large molecules that are complex.
    • Macromolecules have unique properties due to the arrangement of their atoms
    • These molecules are responsible for the assembly and disassembly of macromolecules like enzymes

    Polymers

    • Polymers are long, complex molecules composed of similar building blocks called monomers.
    • Enzymes catalyze the synthesis and breakdown of polymers.
    • Dehydration reaction: synthesis of polymers (removes water forming a new bond)
    • Hydrolysis: breakdown of polymers (adds water to break a bond)

    Carbohydrates

    • Monosaccharides are simple sugars
    • Disaccharides are two monosaccharides joined together
    • Polysaccharides are complex carbohydrates composed of multiple sugar units

    Lipids

    • Lipids are a diverse group of hydrophobic molecules, including fats, phospholipids, and steroids
    • Fats are constructed from glycerol and fatty acids.
    • A fat is a triacylglycerol (three fatty acids attached to glycerol)
    • Phospholipids have a hydrophilic head and two hydrophobic tails.

    Proteins

    • Proteins are polymers constructed from amino acid monomers.
    • A protein's function depends on its specific conformation (shape).
    • Four levels of protein structure: primary, secondary, tertiary, and quaternary.

    Nucleic Acids

    • Nucleic acids store and transmit hereditary information
    • Composed of monomers called nucleotides
    • DNA: deoxyribonucleic acid; RNA: ribonucleic acid

    Metabolism

    • A cell's chemical processes
    • Metabolic pathways can be either anabolic or catabolic depending on whether they build or break down molecules
    • Enzymes speed up metabolic reactions by lowering activation energy.
    • Enzymes are specific for the reactions they catalyze.

    Energy flow and transformation

    • Energy is the capacity to cause change
    • Kinetic energy is the energy of motion. Potential energy is stored energy
    • Chemical energy is a form of potential energy stored in bonds

    Thermodynamics and Energy

    • Thermodynamics is the study of energy transformations
    • The first law of thermodynamics: energy cannot be created or destroyed, only transferred or transformed
    • The second law of thermodynamics: every energy transfer or transformation increases the entropy of the universe.

    Free energy

    • Free energy is a measure of a system's instability; its tendency to change to a more stable state.
    • Exergonic reaction releases free energy; endergonic reaction absorbs free energy.
    • Equilibrium is a state of maximum stability for a system

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