Foundations of Biochemistry and Water, the Solvent of Life

Flashcards covering foundational concepts in biochemistry, including the chemistry of living matter, cellular organization, molecular building blocks, energy transduction, genetic principles, the properties of water, pH and buffers, amino acids, protein structure, and methods for studying proteins.

Biochemistry

The chemistry of living matter.

Living Matter

Characterized by a high degree of complexity and organization, dynamic interactions, systematic energy use, responsiveness to surroundings, and capacity for precise self-replication with evolutionary change.

Cell

The universal building block of living organisms.

Domains of Life

Bacteria, Archaea, and Eukarya

Prokaryotes

Unicellular organisms (Bacteria/Archaea)

Eukarya

Domain containing four Kingdoms: Protista, Fungi, Plantae, and Animalia.

Cell wall

A bacterial cell structure composed of peptidoglycan (sugar + protein) that provides mechanical support.

Cell membrane

A bacterial cell structure composed of lipid + protein that serves as a permeability barrier.

Nucleoid

A bacterial cell structure composed of DNA + protein that stores genetic information.

Ribosomes

Bacterial cell structures composed of RNA + protein responsible for protein synthesis.

Pili

Bacterial cell structures composed of protein; involved in adhesion and conjugation.

Flagella

Bacterial cell structures composed of protein; involved in motility.

Cytoplasm (bacterial)

An aqueous solution within a bacterial cell that is the site of metabolism.

Eukaryotic cells

Cells that have membrane-enclosed organelles that spatially separate energy-yielding and energy-consuming reactions.

Nucleus

The site of DNA metabolism in eukaryotic cells, providing protection for DNA and allowing selective import/export via pores.

Mitochondria

Organelles in animals, plants, and fungi that are locations for many energetic reactions.

Chloroplasts

Organelles found in plants that are locations for many energetic reactions.

Lysosomes

Organelles used for controlled disposal and digestion of un-needed molecules.

Peroxisome

An organelle in animal cells that oxidizes fatty acids.

Vacuole (plant cell)

An organelle in plant cells that degrades and recycles macromolecules and stores metabolites.

Glyoxysome

An organelle in plant cells containing enzymes of the glyoxylate cycle.

Cytoplasm

All the material (biomolecules, water, etc.) in a cell between the plasma membrane and the interiors of organelles.

Cytosol

The highly viscous solvent of the cytoplasm where many reactions take place.

Cytoskeleton

Consists of microtubules, actin filaments, and intermediate filaments; helps maintain cell shape, organization, and allows cellular movement.

Bulk elements

Atoms essential for life, present in organic molecules (H, C, N, O, P, S) and some ions (Na+, Cl-, K+, Ca2+).

Trace elements

Essential metal ions (e.g., Mg2+, Zn2+, Fe2+) that play important roles in metabolism.

Carbon's unique role

Can form single, double, or triple covalent bonds, allowing many different chemical structures and geometrical shapes.

Heterolytic cleavage

More common cleavage of covalent bonds, producing ions (e.g., H+, CH3+) that can react to form new bonds.

Homolytic cleavage

Cleavage of covalent bonds that produces unstable, very reactive radicals that can damage other molecules.

Nucleophiles

Atoms with unpaired or extra electrons (δ- or - charged atoms) that tend to react with electron-poor atoms.

Electrophiles

Atoms with electron deficiency (δ+ or + charged atoms) that tend to react with electron-rich atoms.

Structural isomers

Molecules with the same molecular formula but different bonding arrangements, leading to different physical and chemical properties.

Geometric isomers

Molecules with the same molecular formula and connectivity but different spatial arrangements around a rigid bond (cis and trans isomers), leading to different physical and chemical properties.

Enantiomers

Non-superimposable mirror images of each other, having identical physical and chemical properties (except in chiral environments).

Diastereomers

Non-superimposable structures that are not mirror images of each other, having different physical and chemical properties.

Molecular hierarchy of structure

Cells are built from fundamental building blocks like nucleic acids, amino acids, sugars, and lipids, which assemble into more complex structures.

Energy transductions

The process by which organisms transform energy from one form into another to support life.

Phototrophs

Organisms that obtain energy from sunlight (e.g., plants, algae, cyanobacteria).

Chemotrophs

Organisms that obtain energy from chemicals (e.g., animals, fungi, most bacteria).

Endergonic reactions

Chemical reactions that absorb energy from their surroundings, resulting in products with higher energy than reactants (positive ΔG).

Exergonic reactions

Chemical reactions that release energy into their surroundings, resulting in products with lower energy than reactants (negative ΔG).

Gibbs Free Energy (ΔG)

A thermodynamic quantity that indicates the energy change of a reaction; positive for endergonic, negative for exergonic reactions.

Activation energy (ΔG‡)

The energy barrier that must be overcome for a chemical reaction to start, determining its speed.

Energy coupling

The process of linking an unfavorable (endergonic) reaction with a favorable (exergonic) reaction to allow the unfavorable reaction to occur.

Catalysts

Compounds that increase the rate of a chemical reaction without being consumed in the process, by lowering the activation energy.

Enzymes

Biomolecule catalysts that provide acceleration under mild conditions, high specificity, and possibility for regulation.

Metabolism

The overall set of chemical reactions that occur in a cell, encompassing both catabolic and anabolic pathways.

Catabolic reaction pathways

Exergonic pathways that involve the degradation of molecules (e.g., carbohydrates, lipids, amino acids) to release energy.

Anabolic reaction pathways

Endergonic pathways that involve the synthesis of complex molecules (e.g., carbohydrates, lipids, amino acids) and require energy input.

Miller-Urey experiment

An experiment that demonstrated that some molecules needed for life (e.g., aldehydes, amino acids) could be formed from early atmospheric components in abiotic conditions.

RNA World Hypothesis

The theory that RNA was the original genetic material, capable of acting as both an information carrier and a biocatalyst for its own replication.

Ribozyme

An RNA molecule that has catalytic activity.

Transcription

The process where genetic information in DNA is copied into an RNA form.

Translation

The process where RNA encodes instructions for making proteins.

Random mutations

Changes in DNA that generate genetic diversity in organisms, potentially leading to new attributes and evolutionary advantages.

Endosymbiosis

The evolutionary theory explaining how early eukaryotic cells gained energy-processing organelles (mitochondria and chloroplasts) by engulfing bacteria.

Hydrogen bond

A type of dipole-dipole interaction between a hydrogen donor (-OH, -NH) and a hydrogen acceptor (R-O-R, C=O, R-N=R).

Ionic interactions

Electrostatic interactions between permanently charged atoms or molecules (or between an ion and a permanent dipole).

Hydrophobic effect

The tendency of nonpolar molecules to associate with each other in aqueous solutions, driven by an increase in the entropy of water molecules.

Van der Waals interactions

Weak, short-range attractions between any two atoms due to transient dipoles caused by random variations in electron positions.

Van der Waals radius

The distance at which an atom can come to another atom before their electron clouds repel each other.

Hydrophilic substances

Substances that are charged and/or polar and are good solvents for water (e.g., salts, amino acids, sugars).

Hydrophobic substances

Substances that are nonpolar and are poorly soluble in water (e.g., alkanes, lipids, some gases).

Osmosis

The movement of water into and out of cells across a semipermeable membrane due to differences in solute concentration.

Hypotonic environment

An environment where the fluid outside a cell has a lower solute concentration than the cytosol, causing water to move into the cell.

Isotonic environment

An environment where the fluid outside a cell has the same solute concentration as the cytosol, resulting in equal water movement in and out.

Hypertonic environment

An environment where the fluid outside a cell has a higher solute concentration than the cytosol, causing water to move out of the cell.

Hydronium ion (H3O+)

The product of water molecule dissociation, often represented as a proton (H+).

Hydroxide ion (OH-)

The product of water molecule dissociation.

Proton Hopping (Grotthuss mechanism)

The extremely fast mobility of protons in a hydrogen-bonded network like water, where covalent and hydrogen bonds are interchangeable.

Weak electrolytes

Substances that do not completely dissociate in water.

Acid dissociation constant (Ka)

A measure of the extent to which a weak electrolyte dissociates in water.

Kw (Ion product of water)

The product of the concentrations of H+ and OH- in pure water, equal to 1 x 10^-14 M^2 at 25 °C.

pH

The negative logarithm (base 10) of the hydrogen ion concentration ([H+]), indicating acidity or alkalinity.

pKa

The negative logarithm (base 10) of the acid dissociation constant (Ka), serving as a measure of an acid's strength.

Buffers

Mixtures of weak acids and their conjugate bases that resist changes in pH when acid or base is added, most effective within pKa ± 1.

Buffering capacity

A measure of a buffer's effectiveness, which is greatest when the concentrations of the weak acid and its conjugate base are equal (at pH = pKa).

Bicarbonate buffer system

The primary buffer system that maintains blood pH.

Phosphate buffer system

The primary buffer system that maintains intracellular pH.

Henderson-Hasselbalch Equation

An equation that relates pH, pKa, and the concentrations of the conjugate base ([A-]) and weak acid ([HA]): pH = pKa + log([A-]/[HA]).

Proteins

Main agents of biological function, acting as catalysts, transport molecules, structural components, and motion providers.

Amino acids

The building blocks of proteins, characterized by an alpha-carbon, an acidic carboxyl group, a basic amino group, a hydrogen atom, and a unique side chain (R group).

α-carbon

The central carbon atom of an amino acid to which four substituents are attached.

L-amino acids

The stereoisomeric form of amino acids exclusively used to make proteins.

Side chain (R group)

The unique chemical group attached to the α-carbon of an amino acid, determining its specific properties.

Nonpolar, aliphatic amino acids

Includes Glycine (Gly), Alanine (Ala), Proline (Pro), Valine (Val), Leucine (Leu), Isoleucine (Ile), and Methionine (Met).

Glycine

The only amino acid that is not chiral.

Proline

The only amino acid that does not have a +NH3 α-amino group; has a cyclic structure.

Polar, uncharged amino acids

Includes Serine (Ser), Threonine (Thr), Cysteine (Cys), Asparagine (Asn), and Glutamine (Gln); their side chains can form hydrogen bonds.

Cysteine

A polar, uncharged amino acid capable of forming a disulfide bond with another cysteine residue.

Positively-charged amino acids

Includes Lysine (Lys), Arginine (Arg), and Histidine (His).

Negatively-charged amino acids

Includes Aspartate (Asp) and Glutamate (Glu).

Aromatic amino acids

Includes Phenylalanine (Phe), Tyrosine (Tyr), and Tryptophan (Trp); absorb UV light at 270-280 nm.

Selenocysteine

An uncommon amino acid made from Serine and incorporated into a few proteins.

Post-translational modifications

Chemical alterations to common amino acids after protein synthesis (e.g., methylation, acetylation, phosphorylation, 4-hydroxyproline, γ-carboxyglutamate) often used to regulate protein function.

Cation

An amino acid form in acidic pH where all functional groups are protonated, resulting in a net positive charge.

Anion

An amino acid form in alkaline pH where all functional groups are deprotonated, resulting in a net negative charge.

Zwitterion

A molecule that has both cationic and anionic charged groups simultaneously, typically with a net charge of zero at its isoelectric point.

Isoelectric Point (pI)

The pH at which the net charge of a molecule (like an amino acid or protein) is zero.

Peptide bonds

Amide bonds formed between amino acids in condensation reactions, stabilizing peptides and proteins; are rigid, nearly planar, and typically in the trans configuration.