Biochemistry Key Concepts: Definitions and Terminology
Biochemistry Key Concepts
Lesson 1, 2, and 3:
- Hydrolysis reaction: The cleavage of an element by the addition of the elements of water.
- Amphipathic compounds: Molecules with both polar and nonpolar regions.
- Hydrophobic molecules: Molecules that are not dissolved in water.
- Condensation reaction: The formation of cellular polymers from their subunits by simple reversal of hydrolysis.
- Functional groups: Added groups that confer specific chemical properties on the molecule.
- pH scale: It is a convenient means of designating the concentration of H+ in any aqueous solution in the range between 1.0 M H+ and 1.0 M OH.
- Micelles: Spherical aggregates of amphipathic molecules with their head polar groups facing toward water.
- pKa value: Measure of the tendency of a group to give up a proton.
- Clathrate structures: Highly ordered cagelike shell of water molecules around each nonpolar solute molecule.
- Osmosis: Passive diffusion characterized by the passage of water through the semipermeable membrane from the more dilute solution (hypotonic) to the more concentrated (hypertonic).
- Hydrophilic molecules: Molecules that dissolve easily in water.
- Buffers: Aqueous systems that tend to resist changes in pH when small amounts of acid or base are added.
- Anomeric carbon: Additional asymmetric carbon in a hemiacetal.
- Furanoses: Five-membered hemiacetals.
- Polysaccharides: Long chains of more than 20 monosaccharide units joined by glycosidic bonds.
- Ketose: Monosaccharide in which the carbonyl group is not at the end of the carbon chain.
- Glycosaminoglycan: Linear polymers composed of repeating disaccharide units.
- Pyranoses: Six-membered hemiacetals.
- Aldose: Monosaccharide in which the carbonyl group is at an end of the carbon chain.
- Monosaccharides: Simple sugars.
- Oligosaccharides: Short chains of less than 20 monosaccharide units joined by glycosidic bonds.
- Epimers: Two sugars that differ only in the configuration around one carbon atom.
- Reducing end: The end of a carbohydrate chain with a free anomeric carbon.
- Anomers: Isomeric forms of monosaccharides that differ only in their configuration about the anomeric carbon.
- Sugar derivatives: Sugar in which a hydroxyl group is replaced with another substituent.
- Hemiacetals: Monosaccharide ring structures in which the carbonyl group has formed a covalent bond with the oxygen of a hydroxyl group along the chain.
- Simple triacylglycerols: Triacylglycerols that contain three equal fatty acids.
- Cis configuration: Bond configuration in which the two hydrogen atoms adjacent to the double bond stick out on the same side of the chain.
- Vitamins: Essential organic compounds that the animal organism is not capable of producing itself, although it requires them in small amounts for metabolism.
- Saturated fatty acid: Fatty acid that does not contain double bonds.
- Mixed triacylglycerols: Triacylglycerols that contain two or three different fatty acids.
- Unsaturated fatty acid: Fatty acid that contains one or more double bonds.
- Trans configuration: Bond configuration in which the two hydrogen atoms adjacent to the double bond stick out on opposite sides of the chain.
Lesson 4:
- Isoelectric point: The characteristic pH at which the net electric charge of a molecule is zero.
- Peptides: Molecules formed by less than fifty amino acids joined by peptide bonds.
- Coenzyme: Complex organic or metallo-organic cofactor.
- Zwitterion: Dipolar ion of an amino acid.
- Apoenzyme: The protein part of an holoenzyme.
- Proteins: Molecules formed by more than 50 amino acids joined by peptide bonds.
- Cystine: Two cysteines bound by a disulfide bond.
- Protomers: Each of the identical units of an oligomeric protein.
- Residue: An amino acid unit in a peptide or protein.
- Proteinogenic amino acid: Amino acids which are incorporated biosynthetically into proteins during translation.
- Holoenzyme: A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions.
- Homologous proteins: Members of protein families.
- R groups: Side chain of an amino acid.
- Cofactor: Chemical component that is required for the enzyme’s biological activity.
- Carboxyl-terminal: Amino acid residue at the end of a peptide or protein with a free carboxyl group.
- Orthologs: Homologs that are present in different species.
- Oligopeptide: Molecules formed by less than 15 amino acids joined by peptide bonds.
- Stereochemistry: Atoms configuration, the fixed spatial arrangement of atoms.
- Polypeptide: Molecules formed by 15-50 amino acids joined by peptide bonds.
- Paralogs: Homologs that are present in the same species.
- Amino-terminal: Amino acid residue at the end of a peptide or protein with a free α -amino group.
- Prosthetic groups: Chemical components permanently associated to proteins in addition to amino acids.
- Enantiomers: Stereoisomers that are nonsuperimposable mirror images of each other.
- Multisubunit proteins: Proteins with two or more polypeptides associated noncovalently.
- Allosteric protein: Protein in which the binding of a ligand to one site affects the binding properties of another site on the same protein.
Lesson 6:
- Endergonic reactions: Thermodynamically unfavorable, energy-requiring reactions.
- Exergonic reactions: Thermodynamically favorable, energy-releasing reactions.
- Michaelis constant (Km): Substrate concentration at which V0 is one-half Vmax. It is a measure of the enzyme affinity for the substrate.
- Vmax: The maximum initial rate of the catalyzed reaction.
- Denaturation: Loss of protein structure and function.
- Oxidation reactions: Reactions in which a reduced substrate is oxidized and the produced electrons are used to reduce the electron carrier molecules.
- Reduction reactions: Reactions in which an oxidized substrate is reduced with electrons aported by reduced coenzymes.
- Enzymes: Molecules (usually proteins) that accelerate chemical reactions in order to occur at rates fast enough to sustain life without being consumed in the process.
- Activation energy: Energy needed for the creation of a transition state between reactants and products.
- Free energy content (G): A measure of the “driving force” of a reaction of any closed system.
- Entropy (S): The randomness or disorder of the components of a chemical system.
- Enthalpy (H): The heat content of the reacting system. It reflects the number and kinds of bonds in the reactants and products.
- Catabolic reactions: Reactions that break down organic matter and harvests energy by way of cellular respiration.
- Anabolic reactions: Reactions that use energy to construct components of cells such proteins or nucleic acids from simple molecule s.
Lesson 7 & 8:
- Glucagon: Peptide hormone which regulates the carbohydrate metabolism increasing the breakdown of glycogen from hepatocytes due to a decrease of blood glucose.
- Glucose transporters: Proteins that transport glucose by facilitative diffusion down concentration gradients.
- Sugar nucleotides: Compounds in which the anomeric carbon of a sugar is activated by attachment to a nucleotide through a phosphate ester linkage.
- Glycogenesis: Process of glycogen synthesis, in which glucose molecules are added to chains of glycogen for storage.
- Glycosome: Complex composed by the glycogen molecule, the enzymes involved in its synthesis and lysis and the regulatory enzymes.
- Glycogenolysis: Process of glycogen breakdown, in which glucose molecules are released.
- Insulin: Peptide hormone which regulates the carbohydrate metabolism increasing the uptake of glucose to be stored as glycogen when glucose is in high concentrations in the blood.
- Substrate-level phosphorylations: Reaction that involve soluble enzymes and chemical intermediates to produce ATP by ADP phosphorylation.
- Respiration-linked phosphorylations: Reaction that involve membrane-bound enzymes and transmembrane gradients of protons to produce ATP by ADP phosphorylation.
- Protein phosphatases: Enzymes that catalyze dephosphorylation.
- Glycogenin: Protein that is both the primer the enzyme that catalyzes the assembly of the glycogen molecule.
- Isozymes: Enzymes that catalyze the same reaction but that are encoded by different genes and differs in their kinetic and regulatory properties.
- Protein kinases: Enzymes that catalyze phosphorylation.
Lesson 9 & 10:
- Anaplerotic reactions: replenishing reactions that produce four-carbon intermediates for Krebs cycle by carboxylation of three-carbon compounds.
- Shuttle systems: enzymatic systems that carry reducing equivalents from cytosolic NADH into mitochondria by an indirect route.
- Rotational catalysis: mechanism that indicates that the three active sites of F1 take turns catalyzing ATP synthesis.
- Vectorial reaction: reaction that moves protons in a specific direction from one location to another.
- Mass-action ratio: s the ratio of product concentrations to reactant concentrations at one given time which may be at equilibrium or not.
- Proton pump: integral membrane protein that is capable of moving protons across a biological membrane.
- Proton-motive force: electrochemical energy inherent to the difference in proton concentration and separation of charge across the inner mitochondrial membrane.
- Cellular respiration: the aerobic phase of catabolism in which organic fuel molecules are oxidized to CO2 and water.
- Substrate channeling: process by which the intermediary metabolic product of one enzyme directly to another enzyme without being released into solution.
- Chemiosmotic model: model of ATP synthesis in which the proton-motive force drives the synthesis of ATP as protons flow passively back into the matrix through a proton pore associated with ATP synthase.
Lesson 11 & 12:
- Integral protein: protein that is permanently attached to the biological membrane.
- Amphibolic pathway: metabolic pathway that serves in both catabolic and anabolic processes.
- Serum albumin: blood water-soluble protein that carries free fatty acids.
- α-keto acid: carbon skeleton of an amino acid.
- Pyridoxal phosphate (PLP): prosthetic group derived from pyridoxine (vitamin B6) that functions as an intermediate carrier of amino groups at the active site of aminotransferases.
- Protein turnover: process of synthesis and degradation of cellular proteins.
- Perilipins: family of proteins that restrict access to lipid droplets, preventing untimely lipid mobilization.
- Ping-Pong reactions: reactions in which the first substrate reacts and the product must leave the active site before the second substrate can bind.
- Transamination reaction: reaction between an amino acid and an α-keto acid through which the amino group is transferre from the former to the latter.
Lesson 13:
- Ribosomal RNA: components of ribosomes.
- Renaturation: process by which denatured DNA returns to its native configuration.
- Histones: small, strongly basic proteins that are directly associated with DNA.
- Messenger RNA: RNA carrying the genetic information from DNA to the ribosomes.
- Ribozymes: RNA with enzymatic activity.
- Centromere: sequence of DNA that functions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle.
- Melting point ™: temperature at wich 50% of the DNA is denatured.
- Chromatin: nucleoprotein complexes composed by DNA and proteins.
- Annealing: process by which complementary bases of the single strand pairs or hybridize.
- Mutations: Alterations in DNA structure that produce permanent changes in the genetic information encoded therein.
- Transfer RNA: adapter molecules in protein synthesis.
- Gene: DNA that encodes the primary sequence of some final gene product, which can be either a polypeptide or an RNA with a structural or catalytic function.
- Heterochromatin: highly packed chromatin, usually transcriptionally inactive.
- Chromosome: densely colored bodies seen in the nuclei of dye-stained eukaryotic cells, as visualized using a light microscope.
- Antiparallel DNA: Two chains of a DNA molecule have opposite directions.
- q arm chromosome: Long arm of a chromosome.
- Chromatides: One of the two side by side replicas produced by chromosome replication in mitosis or meiosis.
- Exons: coding DNA segments in genes.
- Nucleosome: fundamental unit of organization upon which the higher-order packing of chromatin is built.
- Transposons: segments of DNA that can move from one location to another in the genome.
- Euchromatin: less dense, transcriptionally active chromatin.
- Genome: the complete set of DNA of an organism, including all of its genes and intergenic DNA.
- Telomeres: sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome.
- p arm chromosome: Short arm of a chromosome.
- Introns: nontranslated (non-coding) DNA segments in genes.
Lesson 14:
- Promoters: specific sequences in the DNA that direct the transcription of adjacent segments of DNA (genes).
- Catenanes: the two topologically interlinked (catenated) circular chromosomes found after DNA replication in prokaryotes.
- Template: single DNA strand (ssDNA) that guides the polymerization reaction during DNA replication or transcription.
- Okazaki fragments: small DNA fragments synthesized during discontinuous DNA replication of the lagging strand.
- Lagging strand: DNA strand in which the 5’à3’ DNA synthesis proceeds in the opposite direction to the replication fork movement.
- Primosome: a functional unit within the replication complex composed by helicase and primase.
- DNA transcription: Process in which we obtain RNA from a mould of DNA.
- Leading strand: DNA strand in which the 5’à3’ DNA synthesis proceeds in the same direction as replication fork movement.
- Replisome: The entire protein complex involved in DNA replication.
- Processivity: The average number of nucleotides added by a polymerase before it dissociates.
- Semiconservative DNA replication: Fifty percent of the new DNA molecules will come from the old DNA molecule per se.
- Nick: site in a DNA strand with a broken phosphodiester bond, leaving a free 3’ hydroxyl and a free 5’ phosphate.
- DNA recombination: Exchange of DNA strands to produce new nucleotide sequence arrangements.
- Primer: strand segment complementary to the template (usually of RNA) with a free 3’-hydroxyl group to which a nucleotide can be added.
Lesson 15:
- Codon: a triplet of nucleotides in mRNA that codes for a specific amino acid or stop signal.
- 5’ cap: residue of 7-methylguanosine linked to the 5’-terminal residue of the mRNA through an unusual 5’,5’-triphosphate linkage.
- Anticodon: a three-base sequence on the tRNA that interacts (base-pair) with mRNA codons.
- Poly(A) “tail”: string of 80 to 250 A residues at the 3’ end of eukaryotic mRNA.
- Lariat structure: structure produced during splicing in which the 5′ end of the intron is linked to the attacking adenosine through a newly formed 2′–5′ phosphodiester linkage.
- Splicing: process by which the introns are removed from the primary transcript and the exons are joined to form a continuous sequence that specifies a functional polypeptide.
- Posttranslational modifications: enzymatic processing reactions that alter some newly made proteins in order to obtain their final biological activity.
- Spliceosome: complex composed by small nuclear ribonucleoproteins that participates in the splicing of nuclear mRNA.
- Open reading frame: a reading frame in mRNA without a termination codon among 50 or more codons.
- Primary transcript: A newly synthesized RNA molecule.
Function of some protein:
- DNA polymerase III: Elongation of the new DNA strand.
- SSB: Binding to single-stranded DNA to prevent renaturation or self-complementary binding.
- DNA polymerase I: Primer excision and DNA repair.
- Topoisomerase IV: separation of the two catenanes during termination of replication.
- Helicase: Separation of both DNA strands.
- Primase: Synthesis of RNA primers.
- DNA ligase: Sealing of nicks produced during the joining of Okazaki fragments and DNA repair.
- DNA polymerase II: DNA repair.
- Topoisomerase II: Relieve of the topological stress created by helicases.