Biochemistry Flashcards
An element of secondary structure, marked by peptide chains lying alongside one another, forming rows or strands.
β-Pleated Sheet
A sphingolipid containing a carbohydrate as a head group.
Cerebroside
Transport of materials through the cell; requires interaction with the cytoplasm and may require transport proteins.
Transcellular Transport
The strand of DNA that is transcribed to form mRNA; also called the antisense strand.
Template Strand
Specialized structural proteins that are involved in cell-to-cell junctions as well as transient cellular interactions; common cell adhesion molecules include cadherins, integrins, and selectins.
Cell Adhesion Molecules
Regaining the correct tertiary structure after denaturation of a protein.
Renaturation
Production of an mRNA molecule from a strand of DNA.
Transcription
A lipid containing a phosphate and an alcohol (glycerol or sphingosine) joined to hydrophobic fatty acid tails.
Phospholipid
Energy-producing metabolic processes that do not require oxygen, including glycolysis and fermentation.
Anaerobic Respiration
The primary energy molecule of the body; it releases energy by breaking the bond with the terminal phosphate to form ADP and an inorganic phosphate.
Adenosine Triphosphate (ATP)
The movement of a molecule against its concentration gradient with energy investment; primary active transport uses ATP, whereas secondary active transport uses a favorable transport gradient of a different molecule.
Active Transport
The first codon in an mRNA molecule that codes for an amino acid (AUG for methionine or N-formylmethionine).
Start Codon
Proteins that are involved in the cytoskeleton and extracellular matrix; they are generally fibrous in nature and include collagen, elastin, keratin, actin, and tubulin.
Structural Proteins
A three-nucleotide sequence on a tRNA molecule that pairs with a corresponding mRNA codon during translation.
Anticodon
A long chain of monosaccharides linked by glycosidic bonds; can be divided into homopolysaccharides (only one type of monosaccharide is used) and heteropolysaccharides (more than one type of monosaccharide is used).
Polysaccharide
The representation of the plasma membrane as a dynamic phospholipid bilayer that interacts with cholesterol and proteins.
Fluid Mosaic Model
Proteins that are involved in cell motility through interactions with structural proteins; motor proteins have ATPase activity and include myosin, kinesin, and dynein.
Motor Proteins
A structural protein around which DNA is coiled in eukaryotic cells.
Histone
The last codon of translation (UAA, UGA, or UAG); release factor binds here, terminating translation.
Stop Codon
Refers to the presence or absence of double bonds in a fatty acid; saturated fatty acids have only single bonds, whereas unsaturated fatty acids have at least one double bond.
Saturation
The conversion of pyruvate to either at the mall and carbon dioxide (yeast) or lactic acid (animal cells); does not require oxygen.
Fermentation
A decrease in enzyme activity that results from the interaction of an inhibitor with an allosteric site; mixed inhibitors bind to the free enzyme and to the substrate-bound enzyme with different affinities. They cannot be overcome by addition of substrate and impact both K{m} and v{max}.
Mixed Inhibition
The synthesis of ketone bodies from the metabolic products of β-oxidation or amino acid metabolism; occurs under conditions of starvation.
Ketogenesis
The primary monosaccharide used for fuel by all cells of the body; has the formula C6H12O6.
Glucose
The simple diffusion of water.
Osmosis
A solution that has a lower concentration than the one to which it is being compared.
Hypotonic
A three-nucleotide sequence in an mRNA molecule that pairs with an appropriate tRNA anticodon during translation.
Codon
The concentration of substrate at which an enzyme runs at half its maximum velocity; a measure of enzyme affinity (the higher the K{m}, the lower the affinity).
K{m}
Being repelled by water; describes nonpolar, uncharged compounds (usually lipids or certain R groups of amino acids).
Hydrophobic
An enzyme that unwinds the double helix of a DNA molecule, allowing replication to take place.
Helicase
The strand of DNA that is synthesized in small fragments, called Okazaki fragments, and then ligated together. The Okazaki fragments are synthesized in the 5’ to 3’ direction, but the overall synthesis is in the 3’ to 5’ direction.
Lagging Stand
The best-supported of the most prominent theories of enzyme specificity; states that the enzyme and the substrate experience a change in conformation during binding to increase complementarity. Usually contrasted with the lock and key theory.
Induced Fit Model
Being attracted to water; describes polar and charged compounds and those that can participate in hydrogen bonding.
Hydrophilic
A molecule composed of more than one amino acid; can be subdivided into dipeptides (two amino acids), tripeptides (three), oligopeptides (up to 20) and polypeptides (more than 20).
Peptide
The major steps in the transfer of genetic information, from transcription of DNA to RNA and translation of that RNA to protein.
Central Dogma of Molecular Biology
Infoldings of the inner mitochondrial membrane that increase the surface area available for electron transport chain complexes.
Cristae
A solution that has a greater concentration than the one to which it is being compared.
Hypertonic
Describes amino acids that can be converted into intermediates that feed into ketogenesis.
Ketogenic
The loss of tertiary structure in a protein, leading to loss of function.
Denaturation
A decrease in enzyme activity that results from the interaction of an inhibitor that binds permanently at either the active site or an allosteric site; in laboratory settings, irreversible inhibitors are sometimes called suicide substrates.
Irreversible Inhibition
A nucleic acid found exclusively in the nucleus that codes for all of the genes necessary for life; transcribed to mRNA and always read 5’ to 3’.
Deoxyribonucleic Acid (DNA)
A decrease in enzyme activity that results from the interaction with an inhibitor at the allosteric site; uncompetitive inhibitors bind only to the substrate-bound enzyme and cannot be overcome by addition of substrate.
Uncompetitive Inhibition
The transport of molecules into a cell through invagination of the cell membrane and the formation of a vesicle; phagocytosis is the endocytosis of solids, pinocytosis is the endocytosis of liquids.
Endocytosis
An inorganic molecule or ion that helps an enzyme carry out its function.
Cofactor
One of the two most prominent theories of enzyme specificity; states that the enzyme and the substrate have a static but complimentary state. Less well-supported than the induced fit model.
Lock and Key Theory
A solution that has the same concentration as the one to which it is being compared.
Isotonic
The lasso-shaped structure formed during the removal of introns in mRNA processing.
Lariat
A special class of membrane receptors with an associated GTP binding protein; activation of a G protein-coupled receptor involves dissociation and GTP hydrolysis.
G Protein-Coupled Receptors
An essential organic coenzyme that assists an enzyme in carrying out its action.
Vitamin
A branched polymer of glucose that represents a storage form of glucose.
Glycogen
A decrease in enzyme activity that results from the interaction of an inhibitor with the active site of an enzyme; competitive inhibition can be overcome by addition of excess substrate.
Competitive Inhibition
An organic molecule that helps an enzyme out its function.
Coenzyme
The process of separating molecules on the basis of size and charge using a porous gel and an electric field; protein electrophoresis generally uses polyacrylamide, while nucleic acid electrophoresis generally uses agarose.
Electrophoresis
A compound that lowers surface tension by acting as a detergent or emulsifier.
Surfactant
The electric potential that results from the unequal distribution of charge around the cell membrane; resting membrane potential which characterizes a cell that has not been stimulated.
Resting Membrane Potential
Dense, tightly coiled DNA that appears dark-colored under the microscope; transcriptionally inactive.
Heterochromatin
Looser, less dense collections of DNA that appear light-colored under the microscope; transcriptionally active.
Euchromatin
A biological molecule with catalytic activity; includes many proteins and some RNA molecules.
Enzyme
The three-dimensional shape of a polypeptide, stabilized by numerous interactions between R groups.
Tertiary Structure
The movement of a molecule down its concentration gradient without energy investment; includes simple and facilitated diffusion and osmosis.
Passive Transport
Transport of materials through the interstitial space without interactions with the cytoplasm or cell membrane.
Paracellular Transport
The transfer of a phosphate group, generally to ATP, which is powered by a gradient formed by oxidation-reduction reactions; occurs in the mitochondria.
Oxidative Phosphorylation
Cell-to-cell junctions that allow for the passage of small molecules between adjacent cells.
Gap Junctions
Metabolic processes that result in the release of energy and the breakdown of molecules.
Catabolism
A decrease in enzyme activity that results from the interaction of an inhibitor with an allosteric site; noncompetitive inhibitors bind equally well to free enzymes and to substrate-bound enzymes. They cannot be overcome by addition of substrate.
Noncompetitive Inhibition
A five-membered ring sugar.
Furanose
An element of secondary structure, marked by clockwise coiling of amino acids around a central axis.
α-Helix
The linear sequence of amino acids in a polypeptide.
Primary Structure
The process of separating components on the basis of their density and resistance to flow by spinning a sample at very high speeds; the most dense components form a solid pellet and the least dense components remain in the supernatant (liquid portion).
Centrifugation
A numerical representation that can be used to determine the prevalent type of biomolecule being used in metabolism; the ratio of carbon dioxide produced to oxygen consumed.
Respiratory Quotient
A method of drawing organic molecules in which horizontal lines are coming out of the page (wedges) and vertical lines are going into the page (dashes).
Fischer Projection
Metabolic processes that result in the consumption of energy and the synthesis of molecules.
Anabolism
A cofactor or coenzyme that is covalently bonded to a protein to permit its function.
Prosthetic Group
The local structure of neighboring amino acids; most common are α-helices and β-pleated sheets.
Secondary Structure
The catalytically active portion of an enzyme.
Active Site
An uneven separation of ions across a biological membrane, resulting in electrical potential energy.
Electrochemical Gradient
The movement of solute molecules through the cell membrane down their concentration gradient through a transport protein or channel; used for ions and large or polar molecules.
Facilitated Diffusion
Enzymes that experience changes in their conformation as a result of interactions at sites other than the active site called allosteric sites; conformational changes may increase or decrease enzyme activity.
Allosteric Enzymes
A sugar that can reduce other compounds and that can be picked up by Tollen’s or Benedict’s reagent.
Reducing Sugar
Production of a protein from an mRNA molecule.
Translation
The amount of energy consumed in a given period of time by an organism while resting.
Basal Metabolic Rate
The inhibition of an enzyme by its product (or a product further down in a metabolic pathway); used to maintain homeostasis.
Feedback Inhibition
Description of the third nucleotide of a codon, which often plays no role in specifying an amino acid; an evolutionary development designed to protect against mutations.
Wobble
A covalent interaction between the -SH groups of two cysteine residues; an element of tertiary and quaternary structure.
Disulfide Bond
An operon that requires an inducer to remove a repressor protein from the operator site to begin transcription of the relevant gene; also called a positive control system.
Inducible System
The strand of DNA that is continuously synthesized in the 5’ to 3’ direction. The template strand is read in the 3’ to 5’ direction.
Leading Strand
A three-carbon alcohol that serves as the backbone for glycerophospholipids, sphingolipids, and triacylglycerols.
Glycerol
A specialized method of separating proteins by their isoelectric point using electrophoresis; the gel is modified to possess a pH gradient.
Isoelectric Focusing
A slightly different version of the same protein, often specific to a given tissue.
Isoform
A lipid with a high melting point that is composed of a very long chain alcohol and a very long chain fatty acid.
Wax
The strand of DNA that is not used as a template during transcription; also called the sense strand.
Coding Strand
The pressure necessary to counteract the effect of an osmotic gradient against pure water; one of the colligative properties; can be thought of as a “sucking” pressure created by solutes drawing in water.
Osmotic Pressure
A method of functionally transferring a compound across a membrane without the actual molecule crossing; common examples are the glycerol 3-phosphate shuttle and the malate-aspartate shuttle.
Shuttle Mechanism
The rapid interconversion between different anomers of a sugar.
Mutarotation
The tendency of unfavorable biological reactions to occur concurrently with favorable reactions, often catalyzed by a single enzyme.
Reaction Coupling
A portion of hnRNA that is spliced together with other exons to form mature mRNA.
Exon
Cell-to-cell junctions that prevent the paracellular transport of materials; tight junctions form a collar around cells and link cells within a single layer.
Tight Junctions
The apparatus used for splicing out introns and bringing exons together during mRNA processing.
Spliceosome
An important metabolic intermediate that can feed into the citric acid cycle, fermentation, or gluconeogenesis.
Pyruvate
The breakdown of glucose into two molecules of pyruvate with the formation of energy carriers (NADH); occurs under both aerobic and anaerobic conditions.
Glycolysis
An enzyme that has already bound a required prosthetic group, coenzyme, or cofactor.
Holoenzyme
A class of lipids build from isoprene moieties; have carbon groups in multiples of 5.
Terpene
Portion of DNA upstream from a gene; contains the TATA box, which is the site where RNA polymerase II binds to start transcription.
Promoter Region
An enzyme devoid of the prosthetic group, coenzyme, or cofactor necessary for normal activity.
Apoenzyme
The method of de novo synthesis of lipids and carbohydrates that relies on gene expression and enzyme specificity rather than the genetic template of DNA or RNA.
Nontemplate Synthesis
The three-step cycle repeated for each amino acid being added to a protein during translation.
Elongation
An energy carrier that accepts electrons and feeds them into the electron transport chain.
Nicotinamide Adenine Dinucleotide (NAD^+)
An energy carrier that accepts electrons and feeds them into the electron transport chain.
Flavin Adenine Dinucleotide (FAD)
The coding pattern of prokaryotes, in which one mRNA may code for multiple proteins.
Polycistronic
Conversion of a biomolecule to its active or usable form, such as activating tRNA with an amino acid or activating a fatty acid with CoA to form fatty acyl-CoA.
Activation
A sphingolipid with a head group composed of sugars; includes cerebrosides and globosides.
Glycosphingolipid
A subtype of of epimers in which the chiral carbon with inverted configuration is the carbonyl carbon (anomeric carbon).
Anomers
Utilization of the proton-motive force generated by the electron transport chain to drive ATP synthesis in oxidative phosphorylation.
Chemiosmotic Coupling
A colorimetric method of determining the concentration of protein in an isolate against a protein standard; relies on a transition of absorption between bound and unbound Coomassie Brilliant Blue dye.
Bradford Protein Assay
A group of 20-carbon molecules that are unsaturated carboxylic acids derived from arachidonic acid; act as paracrine or autocrine hormones.
Prostaglandins
Contents of the inner mitochondrial membrane; includes soluble enzymes of the electron transport chain and mitochondrial DNA.
Matrix
An enzyme that catalyzes the transfer of a functional group.
Transferase
A component of the operon in prokaryotes; a nontranscribable region of DNA that is capable of binding a repressor protein.
Operator Site
The proton concentration gradient across the inner mitochondrial membrane, which is created in the electron transport chain and used in oxidative phosphorylation.
Proton-Motive Force
A specific transferase enzyme that catalyzes the movement of a phosphate group, generally from ATP, to a molecule of interest.
Kinase
A lipid containing a sphingosine or sphingoid backbone bound to fatty acid tails; includes ceramide, sphingomyelins, glycosphingolipids, and gangliosides.
Sphingolipid
An enzyme that is secreted in an inactive form and must be activated by cleavage; common examples are digestive enzymes.
Zymogen
A protein that derives part of its function from covalently attached molecules (prosthetic groups).
Conjugated Protein
The variable component of an amino acid that gives it its identity and chemical properties; also called an R group.
Side Chain
An important metabolic intermediate that links glycolysis and β-oxidation to the citric acid cycle; can also be converted into ketone bodies.
Acetyl-CoA
The transfer of a phosphate group from a high-energy compound to ATP or another compound; occurs in glycolysis.
Substrate-Level Phosphorylation
The enzymes that are primarily responsible for the digestion of proteins in the small intestine; they include trypsin, chymotrypsin, and carboxypeptidases A and B, all of which are secreted as zymogens.
Pancreatic Proteases
A sphingolipid with multiple carbohydrate groups attached as a head group.
Globoside
A collection of several response elements that allow for the control of one gene’s expression by multiple signals.
Enhancer
In prokaryotes, a cluster of genes transcribed as a single mRNA that can be regulated by repressors or inducers, depending on the system.
Operon
A metabolic process that produces NADPH and ribose 5-phosphate for nucleotide synthesis.
Pentose Phosphate Pathway
The description of the structure and function of operons in prokaryotes, in which operons have structural genes, an operator site, a promoter site, and a regulator gene.
Jacob-Monod Model
Transmembrane protein molecules that act enzymatically or as ion channels to participate in signal transduction.
Membrane Receptors
A subtype of diastereomers that differ in absolute configuration at exactly one chiral carbon.
Epimers
The catabolism of fatty acids to acetyl-CoA.
β-Oxidation
Describes amino acids that can be converted into intermediates that feed into gluconeogenesis; all amino acids except leucine and lysine.
Glucogenic
The site of binding for RNA polymerase II during transcription; named for its high concentration of thymine and adenine bases.
TATA box
An enzyme that catalyzes the cleavage or synthesis of a molecule without the addition or loss of water.
Lyase
A sphingolipid with a head group containing an oligosaccharide and one or more N-acetylneuraminic acid (NANA) molecules.
Ganglioside
The reaction between a fatty acid and a strong base, resulting in a negatively charged fatty acid anion bound to a metal ion; creates soap.
Saponification
Increased transcription (and translation) of a gene in response to hormones, growth factors, and other intracellular conditions.
Amplification
The stimulation of an enzyme by an intermediate that precedes the enzyme in a metabolic pathway.
Feed-Forward Activation
An operon that requires a repressor to bind to a corepressor before binding to the operator site to stop transcription of the relevant gene; also called a negative control system.
Repressible System
A lipid containing a glycerol backbone with a phosphate group; bound by ester linkages to two fatty acids.
Glycerophospholipid
An electron donor important in the pentose phosphate pathway that is involved in biosynthesis, oxidative stress, and immune function.
Nicotinamide Adenine Dinucleotide Phosphate (NADP^+)
The bond between the anomeric carbon of a sugar and another molecule.
Glycosidic Linkage
A folded strand of RNA that contains a three-nucleotide anticodon that pairs with an appropriate mRNA codon during translation and is charged with the corresponding amino acid.
Transfer RNA (tRNA)
Proteins that help RNA polymerase II locate and bind to the promoter region of DNA.
Transcription Factors
A sphingophospholipid containing a sphingosine backbone and a phosphate head group.
Sphingomyelin
The production of multiple different but related mRNA molecules from a single primary transcript of hnRNA.
Alternative Splicing
The site of initiation of translation in prokaryotes.
Shine-Dalgarno Sequence
Preprocessed mRNA; converted to mRNA by adding a poly-A tail and 5’ cap and splicing out introns.
Heterogenous Nuclear RNA (hnRNA)
The transport mechanism for lipids within the circulatory and lymphatic systems; includes chylomicrons and VLDL, which transport mostly triacylglycerols, and HDL, IDL, and LDL, which transport mostly cholesterol and cholesteryl esters.
Lipoprotein
The strand of RNA formed after transcription of DNA; moves to the cytoplasm to be translated.
Messenger RNA (mRNA)
A species that binds with the repressor, allowing the complex to bind to the operator region of an operon, stopping transcription of the relevant gene.
Corepressor
A collection of fatty acid or phospholipid molecules oriented to minimize free energy through hydrophobic and hydrophilic interactions; generally a sphere with a hydrophobic core and hydrophilic exterior.
Micelle
The interaction between subunits of a multisubunit protein in which binding of substrate to one subunit increases the affinity of other subunits for the substrate; unbinding of substrate from one subunit decreases the affinity of other subunits for the substrate.
Cooperativity
Cell-to-cell junctions that anchor layers of epithelial cells to one another.
Desmosomes
A less accepted mechanism of ATP synthase activity in which the protons cause a conformational change that releases ATP from ATP synthase.
Conformational Coupling
An enzyme that catalyzes the joining of large polymeric biomolecules, most commonly nucleic acids.
Ligase
Also sometimes called velocity or rate, this is a measure of the catalytic activity of an enzyme. It is often measured as a v{max} and may be analyzed after protein isolation.
Activity
The simplest sphingolipid, with a single hydrogen as its head group.
Ceramide
A glycerol molecule esterified to three fatty acid molecules; the most common form of fat storage within the body.
Triacylglycerol
A portion of hnRNA that is spliced out to form mRNA; remains in the nucleus during processing.
Intron
The pH at which an amino acid is predominantly in zwitterionic form.
Isoelectric Point (pI)
A monocarboxylic acid without additional substituents; fatty acids may be saturated (all single bonds) or unsaturated (contain at least one double bond); natural fatty acids are in the cis conformation.
Fatty Acid
An amide bond between the carboxyl group of one amino acid and the amino group of another amino acid.
Peptide Bond
The structural and enzymatic RNA found in ribosomes that take part in translation.
Ribosomal RNA (rRNA)
The end of translation, in which the ribosome finds a stop codon and release factor binds to it, allowing the peptide to be freed from the ribosome.
Termination
A molecule that contains charges, but is neutral overall. Most often used to describe amino acids.
Zwitterion
A dipolar compound containing an amino group (-NH2) and a carboxyl group (-COOH).
Amino Acid
The interaction between different subunits of a multisubunit protein; stabilized by R group interactions.
Quaternary Structure
A molecule containing four linked rings; cholesterol provides both fluidity and stability to cell membranes and is the precursor for steroid hormones.
Cholesterol
The coding pattern of eukaryotes in which one mRNA molecule codes for only one protein.
Monocistronic
Description of the genetic code, in which more than one codon can specify a single amino acid.
Degenerate
The start of translation, in which the small subunit of the ribosome binds to the mRNA molecule, and the first tRNA (methionine or N-formylmethionine) is bound to the start codon (AUG).
Initiation
The transport of molecules out of a cell by release from a transport vesicle; the vesicle fuses to the cell membrane during secretion.
Exocytosis
An RNA molecule with enzymatic activity.
Ribozyme
A six-membered ring sugar.
Pyranose
The molecule upon which an enzyme acts.
Substrate
A metabolic pathway that produces GTP, energy carriers, and carbon dioxide as it burns acetyl-CoA; also called the Krebs cycle or tricarboxylic acid (TCA) cycle; can share intermediates with many other metabolic processes including fatty acid and cholesterol synthesis, gluconeogenesis, amino acid metabolism, and others.
Citric Acid Cycle
Energy-producing metabolic processes that require oxygen, including the citric acid cycle, electron transport chain, and oxidative phosphorylation.
Aerobic Respiration
The protein that binds to the stop codon during termination of translation.
Release Factor
Protein molecules responsible for the interaction of lipoproteins with cells and the transfer of lipid molecules between lipoproteins; also called apoproteins.
Apolipoprotein
Proteins that assist in protein folding during posttranslational processing.
Chaperones
The production of glucose from other biomolecules; carried out by the liver and kidney.
Gluconeogenesis
The movement of solute molecules through the cell membrane down their concentration gradient without a transport protein; used for small, nonpolar, lipophilic molecules and water.
Simple Diffusion
