Cell Biology Final Exam, Key Concepts

Energy Transformation and Pathways

Energy transformation describes how cells convert energy from one form to another, such as turning chemical energy from food into ATP. Energy pathways are a series of chemical reactions, such as glycolysis and the Krebs cycle, that help cells store, release, and use energy.

Biochemical Signaling and Regulation

Biochemical signaling and regulation involve the processes by which cells communicate and control metabolic pathways using chemical signals and feedback mechanisms.

Pathways of Signal Transduction

Pathways of signal transduction are series of molecular events by which cells respond to external signals, such as hormones or growth factors. These pathways involve the transfer of signals from receptors on the cell surface to target molecules inside the cell, resulting in changes in cell function or gene expression.

Carbohydrate Metabolism

Carbohydrate metabolism is the set of biochemical processes responsible for the formation, breakdown, and interconversion of carbohydrates in living organisms to provide energy.

Electron Transport and ATP Production

Electron transport and ATP production is the final stage of cellular respiration where electrons from NADH and FADH₂ pass through protein complexes in the mitochondrial membrane. This process creates a hydrogen ion gradient, which powers ATP synthase to make ATP from ADP and phosphate. Oxygen acts as the final electron acceptor, making this process vital for energy generation.

ATP Production

ATP production is the creation of energy-carrying ATP molecules, mainly through glycolysis, Krebs cycle, and oxidative phosphorylation.

ATP Synthase

ATP synthase is an enzyme embedded in the inner mitochondrial membrane that uses the proton gradient to make ATP from ADP and inorganic phosphate.

Aerobic Respiration

Aerobic respiration is a process that uses oxygen to completely break down glucose into carbon dioxide and water, generating ATP.

Chemiosmosis

Chemiosmosis is the movement of protons across a membrane, down their electrochemical gradient, which drives the synthesis of ATP.

Electron Transport Chain

The electron transport chain is a series of protein complexes in the inner mitochondrial membrane that transfer electrons, helping create a proton gradient used to produce ATP.

NADH

NADH is a high-energy electron carrier formed during glycolysis and the Krebs cycle, donating electrons to the electron transport chain.

Oxidative Phosphorylation

Oxidative phosphorylation is the process in which ATP is formed as electrons are transferred from NADH or FADH₂ to oxygen by a series of proteins in the inner mitochondrial membrane.

Glycogen Metabolism

Glycogen metabolism refers to how cells store and break down glycogen, a large, branched polymer of glucose. Glycogenesis is the process of making glycogen from glucose, while glycogenolysis is the breakdown of glycogen to release glucose. These pathways help regulate blood sugar and provide energy during fasting or exercise.

Glycolysis and Related Pathways

Glycolysis is a series of biochemical reactions that break down glucose into pyruvate, producing ATP and NADH. Related pathways include processes like the pentose phosphate pathway and fermentation, which also process glucose or its derivatives for energy or biosynthesis.

Glucose

Glucose is a six-carbon sugar molecule that cells use as the primary source of energy.

Glycolysis

Glycolysis is the process in which one molecule of glucose is broken down into two molecules of pyruvate, producing ATP and NADH in the cytoplasm of cells.

Krebs Cycle Steps and Regulation

The Krebs cycle, also called the citric acid cycle, is a series of enzyme-catalyzed steps that oxidize acetyl-CoA to carbon dioxide, generating NADH, FADH2, and GTP/ATP. The activity of key enzymes regulates the cycle, with factors like energy needs and availability of intermediates affecting its speed.

ATP

ATP, or adenosine triphosphate, is the main energy currency of the cell, produced during the Krebs Cycle and other metabolic pathways.

Acetyl-CoA

Acetyl-CoA is a molecule formed from pyruvate that enters the Krebs Cycle, providing the two-carbon group for energy production.

Krebs Cycle

The Krebs Cycle is a series of chemical reactions in the mitochondria that breaks down acetyl-CoA to produce energy, carbon dioxide, and electron carriers.

TCA Cycle

The TCA Cycle, or Tricarboxylic Acid Cycle, is another term for the Krebs Cycle, emphasizing the three carboxyl groups in its key molecules.

Lipid Metabolism

Lipid metabolism includes the chemical pathways by which organisms break down or synthesize lipids, such as fats and oils, to produce energy or to build cell membranes and signaling molecules.

Fatty Acid and Ketone Body Metabolism

Fatty acid and ketone body metabolism refers to the processes by which cells break down fatty acids for energy and produce ketone bodies as alternative energy sources, especially during fasting or carbohydrate scarcity. This includes the breakdown of fats (beta-oxidation), the production of ketone bodies in the liver, and their use by other tissues for energy.

Mitochondria

Mitochondria are cellular organelles responsible for producing ATP and are key sites for beta-oxidation and some steps in ketone body metabolism.

Metabolism and Bioenergetics

Metabolism refers to all chemical reactions in living organisms that maintain life, including breaking down nutrients to produce energy and building complex molecules. Bioenergetics is the study of how organisms manage their energy resources during these metabolic processes.

ATP Structure and Role

Adenosine triphosphate (ATP) is a molecule containing adenine, ribose, and three phosphate groups. ATP serves as the main energy carrier in cells by capturing, storing, and releasing energy needed for cellular activities.

ATP

ATP stands for adenosine triphosphate. It is a molecule used by cells to store and transfer energy needed for many cellular processes.

ATP Synthase

ATP synthase is an enzyme found in mitochondria and chloroplasts that helps generate ATP from ADP and phosphate using biochemical energy.

Cellular Respiration

Cellular respiration is a series of biochemical processes by which cells produce ATP by breaking down nutrients, mainly glucose and oxygen.

Energy Coupling

Energy coupling is the process of linking energy-releasing reactions, such as breakdown of ATP, with energy-consuming processes in the cell.

Energy Currency and Redox Reactions

ATP is often called the energy currency of the cell because it transfers energy for metabolic work. Redox reactions involve the transfer of electrons between molecules, which helps store and release energy during cellular respiration and metabolism.

Coupled Reactions

Coupled reactions occur when a favorable reaction provides energy for an unfavorable reaction, allowing the overall process to happen.

Electron Transfer

Electron transfer is the movement of electrons from one molecule to another, a main feature of many metabolic reactions.

Free Energy

Free energy is the energy in a system that can be used to do work, often measured as Gibbs free energy in biological systems.

NADH

NADH is the reduced form of NAD⁺, carrying high-energy electrons to the electron transport chain.

Redox Potential

Redox potential is the measure of a molecule's ability to accept or donate electrons in a redox reaction.

Redox Reactions

Redox reactions are chemical processes where one molecule loses electrons (is oxidized) and another gains electrons (is reduced). These reactions are important in how cells make and use energy.

Reduction Potential

Reduction potential is the tendency of a molecule to gain electrons and be reduced, usually measured in volts.

Thermodynamics

Thermodynamics is the study of how energy is transferred and transformed in biological systems. It helps explain how chemical reactions in metabolism follow natural laws that guide the direction and efficiency of energy flow.

Activation Energy

Activation energy is the minimum amount of energy needed to start a chemical reaction. Enzymes in cells lower the activation energy to speed up reactions.

First Law of Thermodynamics

This law states that energy cannot be created or destroyed, only converted from one form to another. In metabolism, the total energy in a biological system remains constant during chemical transformations.

Reaction Spontaneity

Reaction spontaneity refers to whether a reaction will proceed without continuous energy input. If ΔG is negative, the reaction is considered spontaneous.

Photosynthetic Energy Pathways

Photosynthetic energy pathways are the processes in which plants, algae, and some bacteria capture light energy and convert it into chemical energy, primarily in the form of glucose, through photosynthesis.

Carbon Fixation and the Calvin Cycle

Carbon fixation is the process of converting inorganic carbon dioxide into organic molecules. The Calvin cycle is a series of enzyme-driven reactions in the chloroplast that uses ATP and NADPH from the light-dependent reactions to synthesize sugars from carbon dioxide.

Glyceraldehyde-3-Phosphate (G3P)

G3P is a three-carbon sugar formed in the Calvin Cycle after 3-PGA is converted using ATP and NADPH. It serves as a building block to produce glucose and other carbohydrates.

NADPH

NADPH is an electron carrier molecule that provides the reducing power needed to convert 3-PGA into G3P in the Calvin cycle.

Light-Dependent Photosynthesis

Light-dependent photosynthesis is the stage of photosynthesis that requires sunlight. In this process, light energy is absorbed by chlorophyll and converted into chemical energy in the form of ATP and NADPH. This occurs in the thylakoid membranes of chloroplasts and produces oxygen as a byproduct.

ATP Synthase

ATP synthase is an enzyme in the thylakoid membrane that uses the proton gradient to produce ATP from ADP and inorganic phosphate.

Molecular Components and Interactions

Molecular components refer to the basic molecules, such as proteins, lipids, nucleic acids, and carbohydrates, that form cells and living systems. Interactions among these molecules include binding, chemical reactions, and signals, which allow various biological processes to occur inside an organism.

Biological Molecules

Biological molecules are chemical compounds found in living organisms. They include carbohydrates, proteins, lipids, and nucleic acids. These molecules perform essential functions in cells, such as providing energy, building structures, and storing genetic information.

Amino Acid Properties and Protein Structure

Amino acids are small molecules with differing side chains that link to form proteins. Protein structure involves how chains fold and arrange, which is crucial for their role as enzymes, transporters, and structural molecules.

Active Site

The active site of a protein, usually an enzyme, is the region where substrate molecules bind and chemical reactions occur.

Amino Acid

Amino acids are organic molecules that serve as the building blocks of proteins, each containing an amino group, a carboxyl group, a hydrogen atom, and a unique side chain attached to a central carbon atom.

Hydrogen Bond

A hydrogen bond is a weak attraction between a hydrogen atom and an electronegative atom, important for stabilizing protein structures.

Primary Structure

Primary structure refers to the specific linear sequence of amino acids in a protein or polypeptide chain.

Side Chain

A side chain is the variable group attached to the central carbon of an amino acid, also called the R-group, influencing the amino acid's behavior.

Lipid Structure and Function

Lipid structure is based on long hydrocarbon chains or rings, making them mostly nonpolar, and their functions include energy storage, making up cell membranes, and serving as signaling molecules.

Lipid Bilayer

A lipid bilayer is a double layer of phospholipids that forms the basic structure of cell membranes, with hydrophobic tails inside and hydrophilic heads outside.

Membrane Structure

Membrane structure refers to the arrangement of lipids, proteins, and carbohydrates in the cell membrane, with the lipid bilayer providing the basic framework.

Molecular Building Blocks

Molecular building blocks are simple chemical units like sugars, fatty acids, amino acids, and nucleotides that combine to create larger biological molecules essential for life.

Nucleotides

Nucleotides are the monomers of nucleic acids, comprised of a phosphate group, a five-carbon sugar, and a nitrogen-containing base.

Phosphate Group

A phosphate group is a chemical group made of a phosphorus atom bonded to four oxygen atoms, important for energy transfer and as a component of nucleotides.

Phosphodiester Bond

A phosphodiester bond is a chemical bond that connects nucleotides together in the backbone of DNA and RNA, linking the phosphate group of one nucleotide to the sugar of another.

Water

Water is a small molecule composed of two hydrogen atoms and one oxygen atom (H₂O), and it acts as a universal solvent in biological systems.

Nucleotides and Nucleic Acids

Nucleotides are molecules made of a sugar, phosphate group, and nitrogenous base; they join to form nucleic acids like DNA and RNA, which store and transfer genetic information.

Complementary Base Pairing

Complementary base pairing is the specific hydrogen bonding between nitrogenous bases. Adenine pairs with thymine (or uracil), and guanine pairs with cytosine.

DNA

DNA, or deoxyribonucleic acid, is a double-stranded nucleic acid that stores genetic information in cells. It contains the bases adenine, cytosine, guanine, and thymine.

Double Helix

A double helix is the twisted ladder-like shape formed by two strands of DNA coiled around each other.

Nucleotide

A nucleotide is a molecule composed of a nitrogenous base, a five-carbon sugar (either ribose or deoxyribose), and one or more phosphate groups. It is the basic building block of nucleic acids like DNA and RNA.

Phosphodiester Bond

A phosphodiester bond is a chemical link between the phosphate group of one nucleotide and the sugar of another, forming the backbone of nucleic acids.

RNA

RNA, or ribonucleic acid, is usually a single-stranded nucleic acid involved in coding, decoding, regulation, and expression of genes. It contains the bases adenine, cytosine, guanine, and uracil.

Enzymes and Enzyme Kinetics

Enzymes are proteins that speed up chemical reactions in the body by lowering the activation energy. Enzyme kinetics is the study of how enzymes bind to substrates and turn them into products, focusing on the rates of these reactions.

Enzyme Kinetics and Inhibition

Enzyme kinetics is the study of how fast enzyme-catalyzed reactions occur and what factors control these rates, such as substrate concentration and temperature. Inhibition refers to processes that decrease or stop enzyme activity, often through molecules that specifically block the enzyme's active site or alter its shape, thus slowing or preventing the reaction.

Enzyme Activity

Enzyme activity measures how effectively an enzyme catalyzes a reaction, usually expressed as the amount of product formed per unit time.

Reaction Rate

Reaction rate is the change in concentration of reactants or products per unit time in a chemical reaction.

Enzyme Structure and Catalysis

Enzyme structure refers to the specific three-dimensional shape formed by proteins that allows them to function as enzymes. Catalysis is the process by which enzymes increase the speed of chemical reactions without being consumed. The unique structure of an enzyme enables it to bind to specific molecules, called substrates, and convert them into products through a series of controlled chemical steps.

Activation Energy

Activation energy is the minimum amount of energy required to start a chemical reaction.

Active Site

The active site is the specific region of an enzyme where the substrate binds and the chemical reaction takes place.

Induced Fit

Induced fit is the model describing how an enzyme changes shape slightly to better fit its substrate when they bind together.

Specificity

Specificity refers to the ability of an enzyme to selectively bind to a particular substrate and catalyze only a particular reaction.

Vitamins and Cofactors

Vitamins are organic compounds that organisms need in small amounts for normal health. Cofactors are non-protein molecules, sometimes derived from vitamins, that help enzymes perform their functions.

Coenzymes and Cofactors

Coenzymes and cofactors are non-protein molecules that assist enzymes in catalyzing biochemical reactions. Coenzymes are organic molecules, often derived from vitamins, that temporarily bind to enzymes. Cofactors can be either inorganic ions (like magnesium or zinc) or organic molecules, helping enzymes function properly by stabilizing their structure or participating in the reaction.

NADH

NADH is the reduced form of NAD⁺ and carries electrons to the electron transport chain during cellular respiration.

Biochemical Processes and Molecular Interactions

Biochemical processes are chemical reactions that take place inside living cells, such as breaking down nutrients or synthesizing proteins. Molecular interactions refer to how molecules like proteins, nucleic acids, and small molecules interact and recognize each other, which is essential for a cell’s function and survival.

Cell Chemistry

Cell chemistry refers to the study of the chemical processes and molecules, such as water, ions, proteins, carbohydrates, lipids, and nucleic acids, that are necessary for cell structure, function, and survival.

Biological Macromolecules

Biological macromolecules are large, complex molecules found in living organisms. The main types include carbohydrates, proteins, lipids, and nucleic acids. They serve critical structural and functional roles in the cell, such as energy storage, building cellular structures, performing biochemical reactions, and carrying genetic information.

Glycosidic Bond

A glycosidic bond is a type of covalent bond that links one sugar molecule to another in carbohydrates.

Lipids

Lipids are hydrophobic, energy-rich molecules that include fats, oils, phospholipids, and steroids. They store energy and form cell membranes.

Nucleic Acids

Nucleic acids are genetic macromolecules, such as DNA and RNA, composed of nucleotide chains that store and transmit genetic information.

Peptide Bond

A peptide bond is a strong covalent bond joining two amino acids together between the amino group of one and the carboxyl group of another.

Phosphodiester Bond

A phosphodiester bond joins two nucleotides together in nucleic acids by connecting the phosphate group of one and the sugar backbone of the next.

Proteins

Proteins are large biomolecules made of amino acids that perform many functions in cells, including catalysis, support, transport, and communication.

Chemical Characteristics of the Cell

Chemical characteristics of the cell refer to the unique molecular composition and properties found within living cells. These include the presence of elements like carbon, hydrogen, oxygen, and nitrogen, as well as the organization and interactions of molecules such as water, ions, and organic compounds, which all contribute to cellular functions and processes.

Chemical Bonds

Chemical bonds are the connections between atoms or molecules that hold them together. They include covalent, ionic, and hydrogen bonds.

Covalent Bonds

Covalent bonds are chemical bonds formed when two atoms share pairs of electrons. They are strong and common in organic molecules.

Hydrogen Bonds

Hydrogen bonds are weak attractions between a hydrogen atom in one molecule and an electronegative atom, like oxygen or nitrogen, in another molecule.

Water

Water is a molecule made up of two hydrogen atoms bonded to one oxygen atom. It is the most abundant compound in cells and acts as a solvent for many biochemical reactions.

Cellular Energy Conversion and Metabolism

Cellular energy conversion and metabolism refer to the processes by which cells transform nutrients into usable energy and carry out chemical reactions necessary for growth, maintenance, and function.

Cellular Respiration (Glucose Catabolism)

Cellular respiration is the metabolic process by which cells break down glucose molecules to produce energy in the form of ATP. This process uses oxygen and releases carbon dioxide and water as byproducts.

ATP Synthase

ATP Synthase is an enzyme found in the inner mitochondrial membrane that uses the energy from a proton gradient to synthesize ATP from ADP and inorganic phosphate.