CH 2: Cell Chemistry and Bioenergetics Flashcards

Flashcards for key vocabulary and concepts from the Cell Chemistry and Bioenergetics lecture.

Macromolecules

Enormous molecules that are polymeric in nature, meaning they are composed of repeating subunits. These large molecules possess unique properties that enable essential biological processes such as cell growth and reproduction.

Monomer

A small organic molecule that serves as a building block or subunit to construct giant polymeric macromolecules. These subunits link together to form larger structures.

Organic Molecules

Carbon compounds synthesized by cells, distinguished by their carbon-based structure. These molecules form the basis of living organisms and their biological processes.

Inorganic Molecules

Molecules not based on carbon, generally simpler in structure compared to organic molecules. Water is a primary example, essential for life processes.

Sugars

One of the four major families of small organic molecules; serve as building blocks for polysaccharides (complex carbohydrates), glycogen (energy storage in animals), and starch (energy storage in plants). Examples include glucose, fructose, and ribose.

Fatty Acids

One of the four major families of small organic molecules; act as building blocks for fats and membrane lipids. These are composed of a polar head and a nonpolar hydrocarbon tail.

Nucleotides

One of the four major families of small organic molecules; the building blocks for nucleic acids (DNA and RNA). Each nucleotide consists of a sugar, a phosphate group, and a nitrogenous base.

Amino Acids

One of the four major families of small organic molecules; the building blocks for proteins. Each amino acid contains an amino group, a carboxyl group, and a unique side chain (R group).

the four types of the small organic building blocks of the cell and their larger organic counterparts

are sugars, fatty acids, amino acids, and nucleotides. Which turn into Polysaccharides, Glycogen and Starch, fats and membrane lipids, proteins, and nucleic acids.

The four elements that make up 96.5% of an organism’s weight

These elements are Carbon (C), Hydrogen (H), Nitrogen (N), and Oxygen (O), and they constitute the majority of an organism’s mass.

Covalent Bonds

Chemical bonds that involve the sharing of electrons between atoms, linking them together to form molecules. These bonds are strong and crucial for the stability of biological molecules.

Noncovalent Bonds

Weaker chemical bonds that allow molecules to interact and associate reversibly. Critical for many biological functions, including molecular recognition and temporary interactions.

Electrostatic Attractions (Ionic Bonds)

Strong when atoms are fully charged or ionized, but their strength is significantly reduced in the presence of water. These attractions occur between oppositely charged ions.

Hydrogen Bond

A relatively weak bond formed through the attraction between a hydrogen atom with a partial positive charge and an electronegative atom (such as oxygen or nitrogen) with a partial negative charge.

Van der Waals Attraction

A weak, short-range attraction that occurs between any two atoms close to each other, resulting from temporary fluctuations in electron distribution. These attractions contribute to the overall stability of molecular structures.

bonds sorted by strength

1. Covalent Bonds: Strongest bonds, involving the sharing of electrons between atoms.

2. Ionic Bonds (Electrostatic Attractions): Strong when atoms are fully charged or ionized; significant in the absence of water.

3. Hydrogen Bonds: Weaker bonds formed by the attraction between a hydrogen atom and an electronegative atom.

4. Van der Waals Attractions: Weakest bonds, resulting from temporary fluctuations in electron distribution.

Water and Water Structure

Water is a polar molecule with a bent structure, enabling it to form extensive hydrogen bonds. This structure gives water its unique properties as a solvent and its high surface tension, crucial for life.

Hydrophilic Molecules

Polar or charged molecules that readily dissolve in water by forming hydrogen bonds with water molecules. Examples include ions, sugars, and some proteins.

Hydrophobic Molecules

Nonpolar molecules that do not dissolve in water and tend to cluster together in aqueous environments due to the hydrophobic effect.

Water as a Solvent

The polarity of water makes it an excellent solvent for polar and ionic compounds, allowing biochemical reactions to occur in cells. Water can also hydrate ions, stabilizing them in solution.

Weak Noncovalent Chemical Bonds

Weak, noncovalent interactions including hydrogen bonds, van der Waals forces, and hydrophobic interactions. They are crucial for transient interactions in biological systems, such as protein-ligand binding and membrane formation.

Sulfhydryl Group

The * (-SH) is a chemical group found in thiols and is significant in protein structure. Two * can oxidize to form a disulfide bond (-S-S-), which stabilizes protein folding.

Carbon Skeletons

Chains of carbon atoms that form the structural backbones of organic molecules. These skeletons can be linear, branched, or cyclic, providing versatile frameworks for building complex molecules.

Why do organics use carbon atoms?

Carbon's tetravalent nature allows it to form stable covalent bonds with other carbon atoms and diverse elements like hydrogen, oxygen, nitrogen, and sulfur, enabling the creation of a vast array of organic compounds.

C-H Compounds

Compounds containing only carbon and hydrogen, which are nonpolar and hydrophobic due to the similar electronegativity of C and H. These compounds are prevalent in fats and oils.

Alternating Double Bonds

Double bonds alternating with single bonds in a carbon chain create a conjugated system, allowing for electron delocalization and resonance. This affects the molecule's stability and chemical properties, as seen in aromatic compounds.

C-O Compounds

Carbon-oxygen bonds are polar due to oxygen's higher electronegativity. These compounds include alcohols, aldehydes, ketones, and carboxylic acids, which are often hydrophilic and reactive.

C-N Compounds

Carbon-nitrogen bonds are polar and found in amines, amides, and amino acids. Amines are basic, while amides are neutral; amino acids are amphoteric, containing both amine and carboxylic acid groups.

Phosphates

Groups (PO4^3-) are negatively charged and crucial in energy transfer (ATP), DNA, and RNA. They can form phosphoester bonds with alcohols and phosphoanhydride bonds with other phosphates.

Acids

Substances that release protons (H+) when dissolved in water, increasing the concentration of hydronium ions (H3O+). Strong * completely dissociate in water.

Acids

* are substances that donate protons (H+) when dissolved in water, increasing the concentration of hydronium ions (H3O+). Strong acids completely dissociate in water.

Bases

Substances that accept protons (H+) when dissolved in water, decreasing the concentration of hydronium ions (H3O+). Strong * completely dissociate in water.

Hydrogen Ion Exchange

Involves the reversible transfer of protons between molecules, which influences pH levels and the activity of biological molecules. This exchange is crucial for maintaining acid-base balance in cells.

pH

A measure of the acidity or basicity of a solution, defined as the negative logarithm of the hydrogen ion concentration: pH = -log[H^+]. A pH of 7 is neutral, below 7 is acidic, and above 7 is basic.

Condensation Reaction

A chemical reaction in which a molecule of water is lost with each subunit added to a polymer. This process builds larger molecules from smaller ones.

Hydrolysis

The chemical breakdown of a compound due to reaction with water. This reaction breaks down polymers into smaller subunits.

Enzymes

Specialized biological catalysts, usually proteins (sometimes ribozymes formed by RNA), that accelerate chemical reactions by lowering the activation energy required. They are essential for most biochemical processes.

Enzymes as Catalysts

_ are biological catalysts, often proteins or ribozymes (RNA), that speed up chemical reactions in cells. They lower the activation energy, which increases reaction rates under normal conditions, and do not change the equilibrium point of the reaction.

Substrates

Molecules to which an enzyme binds tightly, reducing the activation energy of a particular chemical reaction and facilitating the formation of products.

Catabolic Pathways

These pathways break down foodstuff into smaller molecules, generating useful energy and building blocks for other molecules.

Anabolic (Biosynthetic) Pathways

These pathways use small molecules and energy to synthesize the many other molecules that form the cell, including proteins, nucleic acids, and lipids.

Cell Metabolism

The sum of all chemical reactions in a cell, including both catabolic and anabolic pathways. This includes processes that provide energy and molecular building blocks for cellular functions.

Entropy

The amount of disorder in a system. In biological contexts, it refers to the tendency of systems to move towards increased disorder, which impacts energy transformations.

First Law of Thermodynamics

Energy can be converted from one form to another, but it cannot be created or destroyed. This principle governs all energy transformations in biological systems.

Photosynthesis and Respiration

Complementary processes where photosynthesis uses sunlight to convert carbon dioxide and water into glucose and oxygen, while respiration uses oxygen to break down glucose into carbon dioxide and water, releasing energy. The products of one process serve as the reactants for the other, creating a cycle of energy and matter.

Oxidation

The removal of electrons from a molecule; a reaction in which electrons are transferred from one atom to another. This process often involves the addition of oxygen or removal of hydrogen.

Reduction

The addition of electrons to a molecule; a reaction in which electrons are transferred from one atom to another. This process often involves the addition of hydrogen or removal of oxygen.

aerobic oxidation

A set of metabolic reactions that uses oxygen (O_2) to fully oxidize molecules, such as glucose, to carbon dioxide and water, releasing energy in the form of ATP. This process occurs in the mitochondria of eukaryotic cells.

anaerobic oxidation

A metabolic process that oxidizes molecules without using oxygen (O*2). It occurs in the absence of oxygen and typically yields less energy (ATP). Examples include fermentation and * -respiration, essential for energy production in oxygen-lacking environments or organisms.

Free Energy

Energy that can be harnessed to do work or drive chemical reactions in a cell. This energy determines the spontaneity of a reaction.

Activation Energy

The minimum amount of energy required to initiate a chemical reaction. It represents the energy barrier that must be overcome for reactants to transition into products. Enzymes lower _ by providing an alternative reaction pathway or stabilizing the transition state, thereby increasing the reaction rate.

∆G (Delta G)

Free-energy change, a direct measure of the amount of disorder (entropy) created in the universe when a reaction takes place. It determines the spontaneity of a reaction; a negative ∆G indicates a spontaneous reaction that releases energy (exergonic), while a positive ∆G indicates a non-spontaneous reaction that requires energy input (endergonic).

∆G°

Standard free-energy change of a reaction, at a standard condition where the concentrations of all reactants are set to 1 mole/liter. It provides a reference point for comparing the spontaneity of different reactions.

Equilibrium Constant (K)

The ratio of product to substrate when a chemical equilibrium is attained. The can be expressed as: K=[Products]/[Substrates], indicating the ratio of products to substrates at equilibrium.

Activated Carrier Molecules

Molecules that store energy in an easily exchangeable form, either as a readily transferable chemical group or as electrons held at a high energy level. These molecules are essential for driving various cellular processes.

ATP (Adenosine Triphosphate)

* is the main energy currency in cells, powering biological processes through high-energy phosphate bonds. Hydrolysis of * to ADP or AMP releases energy for cellular activities like muscle contraction and chemical synthesis.

NAD+ (Nicotinamide Adenine Dinucleotide)

An electron carrier; as part of an enzyme-catalyzed reaction in which a substrate molecule is oxidized, _ molecule picks up a “packet of energy” corresponding to two electrons plus a proton (H+).

NADP+ (Nicotinamide Adenine Dinucleotide Phosphate)

_ is an electron carrier that accepts two electrons and a proton (H+) to become NADPH, providing reducing power for anabolic reactions like lipid and nucleic acid synthesis.

Glycolysis

The major process for oxidizing sugars, producing ATP without the involvement of molecular oxygen (O2 gas). This pathway is a key step in energy production in many organisms.

Fermentations

Energy-yielding pathways that occur in the absence of oxygen, allowing cells to produce ATP in anaerobic conditions.

Adipocytes

Specialized fat cells where animals store fatty acids as fat droplets composed of water-insoluble triacylglycerols (also called triglycerides). These cells serve as a major energy reserve.

Citric Acid Cycle

Also known as the tricarboxylic acid cycle or the Krebs cycle, it accounts for about two-thirds of the total oxidation of carbon compounds in most cells, and its major end products are CO2 and high-energy electrons in the form of NADH.

Oxidative Phosphorylation

Energy released by chain of electron transfers in the electron-transport chain is used to pump H+ ions (protons) across the membrane to generate ATP. This process is the primary source of ATP in aerobic respiration.

Hydrogen Bonds in Water

Between water molecules give water its unique properties, such as high surface tension and cohesion. These bonds are crucial for life as they affect temperature regulation and act as a versatile solvent.

Cation-$\pi$ Interactions

Noncovalent interaction between a cation and the face of a $\pi$ system (e.g. an aromatic ring). It is significant in protein structure, enzyme-substrate interactions, and molecular recognition.

Electrostatic Attractions in Water

The strength of electrostatic attractions (ionic bonds) is significantly reduced in water due to water's polarity. However, they still play a role in stabilizing molecular structures, especially in hydrophobic regions of proteins.

Monosaccharides

Simple sugars with the general formula (CH2O)n, where n is typically 3 to 7. Examples include glucose, fructose, and galactose, which serve as energy sources and building blocks for larger carbohydrates.

Ring Formations

Monosaccharides often exist in ring forms in aqueous solutions. The linear form cyclizes to form either a furanose (five-membered ring) or a pyranose (six-membered ring), affecting their reactivity and stability.

Isomers

Molecules with the same chemical formula but different structural arrangements. can have different chemical and physical properties, affecting their biological roles.

$\alpha$ and $\beta$ Links

Refer to the stereochemical configuration of the glycosidic bond in carbohydrates. An $\alpha$ link means the -OH group on carbon-1 is below the plane of the ring, while a $\beta$ link means it is above.

Sugar Derivatives

Modified sugars with additional functional groups, such as amino sugars (e.g., glucosamine) and acidic sugars (e.g., glucuronic acid). These derivatives play structural roles and are involved in cell signaling.

Disaccharides

Carbohydrates composed of two monosaccharides linked by a glycosidic bond. Common examples include sucrose (glucose + fructose) and lactose (glucose + galactose).

Oligosaccharides and Polysaccharides

Oligosaccharides contain a few monosaccharides, while contain many. Polysaccharides like starch, glycogen, and cellulose serve as energy storage and structural components in cells.

Complex Oligosaccharides

Attached to proteins (glycoproteins) or lipids (glycolipids) on cell surfaces, involved in cell recognition, signaling, and immune responses. Their diverse structures enable specific biological interactions.

Fatty Acids

Carboxylic acids with long hydrocarbon chains, classified as saturated (no double bonds) or unsaturated (one or more double bonds). They are essential components of lipids and serve as energy stores.

Triacylglycerols

Also known as triglycerides, are formed from a glycerol molecule esterified with three fatty acids. They are the main constituents of body fat in animals and are used for energy storage.

Carboxyl Group

Functional group (-COOH) found in organic acids like fatty acids and amino acids. It can donate a proton, making the molecule acidic.

Phospholipids

Lipids containing a phosphate group, which makes them amphipathic. They are major components of cell membranes, forming lipid bilayers.

Lipid Aggregates

Structures formed by lipids in aqueous solutions, such as micelles and bilayers. These aggregates are stabilized by hydrophobic interactions and are critical for membrane structure.

Other Lipids

Include glycolipids (lipids with attached carbohydrates), steroids, and waxes. These have diverse functions, such as cell signaling, membrane structure, and protection.

Polyisoprenoids

Lipids synthesized from isoprene units, such as terpenes and carotenoids. They play roles in pigmentation, vitamin synthesis, and electron transport.

Steroids

Lipids characterized by a four-ring structure. Examples include cholesterol, hormones like testosterone and estrogen, and bile acids. They have roles in membrane structure, signaling, and digestion.

Glycolipids

Composed of a lipid and a carbohydrate, present on cell membranes. They are involved in cell recognition and signaling.

Phosphates

Involved in energy transfer (ATP), DNA, and RNA. They can form phosphoester bonds with alcohols and phosphoanhydride bonds with other phosphates.

Sugars Nomenclature

are named based on the number of carbon atoms (e.g., triose, tetrose, pentose, hexose) and the presence of aldehyde (aldose) or ketone (ketose) groups. For example, glucose is an aldohexose.

Nucleotides and Derivatives Other Functions

Serve as energy carriers (ATP, GTP), signaling molecules (cAMP, cGMP), and enzyme cofactors (NAD, FAD). They participate in metabolic regulation and signal transduction.

Seven Most Common Functional Groups in Biology

Hydroxyl (-OH), carbonyl (=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (-PO4^3-), and methyl (-CH3). These groups dictate the chemical properties and reactivity of organic molecules.